1. Installing and Loading Packages

This first block of code installs and loads all the libraries needed for the analysis. The include=FALSE option in the block header ensures that the installation commands and loading messages will not appear in the final HTML report, making it cleaner.

2. Data Loading and Preparation

Here, we load the raw count table and gene annotations directly from the GEO repository.

# load counts table from GEO
urld <- "https://www.ncbi.nlm.nih.gov/geo/download/?format=file&type=rnaseq_counts"
path <- paste(urld, "acc=GSE117769", "file=GSE117769_raw_counts_GRCh38.p13_NCBI.tsv.gz", sep="&");
gset<- as.matrix(data.table::fread(path, header=T, colClasses="integer"), rownames="GeneID")

# load gene annotations
apath <- paste(urld, "type=rnaseq_counts", "file=Human.GRCh38.p13.annot.tsv.gz", sep="&")
annot <- data.table::fread(apath, header=T, quote="", stringsAsFactors=F, data.table=F)

# Load the dataset
gse <- getGEO("GSE117769", GSEMatrix = TRUE, AnnotGPL = TRUE)
## Found 1 file(s)
## GSE117769_series_matrix.txt.gz
## Annotation GPL not available, so will use submitter GPL instead
gse <- gse[[1]]

# Extract phenotype data
pheno_data <- pData(gse)
pheno_data <- pheno_data[, c("title", "geo_accession", "characteristics_ch1.6")]

3. Selection of 433 genes

Gene selection performed by text mining and functional enrichment.

#Define genes of interest
genes_of_interest <- c(
  "ABCB11", "ABCD2", "ACE", "ACKR2", "ACP5", "ACP7", "ADAMTS9", "ADCY7", "ADGRL2", "ADIPOQ", "AHR", "AIM2", "AKAP13", "ALB", "ANKRD55", "ANXA1",
  "APOL1", "APOL6", "AQP1", "AREG", "ARHGEF3", "ATG16L1", "ATG5", "ATOX1", "ATXN2L", "BEND2", "BGLAP", "BMP2", "BMP7", "BNIP3L", "BRAF", "BTG1",
  "C15ORF48", "C7ORF57", "CALD1", "CAPS2", "CARD9", "CASP1", "CASP10", "CAST", "CCL2", "CCL20", "CCL25", "CCL3", "CCL5", "CCND1", "CCND3", "CCR2",
  "CCR6", "CCR7", "CCRL2", "CD14", "CD160", "CD19", "CD274", "CD28", "CD36", "CD38", "CD3E", "CD4", "CD40", "CD40LG", "CD52", "CD63", "CD68",
  "CD69", "CD80", "CD83", "CD86", "CD8A", "CD8B", "CDC42BPB", "CEBPA", "CEBPG", "CENPK", "CLEC2B", "CLEC4D", "CLIC3", "CMAHP", "CMTM2",
  "COL1A1", "COX2", "CRB1", "CREM", "CRP", "CSF2", "CSMD1", "CSN3", "CSNK1A1", "CTLA4", "CTSB", "CTSK", "CUX1", "CX3CR1", "CXCL10", "CXCL13",
  "CXCL16", "CXCL2", "CXCL8", "CXCR2", "CYCS", "CYP1A1", "CYP4F22", "DDIT3", "DDX60", "DKK1", "DLAT", "DNAJA2", "DNAJB6", "DUSP4", "DYSF",
  "EDNRA", "EFCAB13", "EFCAB7", "EGF", "EGFR", "EGR3", "EIF5B", "ENO1", "EOMES", "ERAP1", "ERAP2", "ERN1", "ERP44", "EZH2", "FAXDC2", "FCGR1A",
  "FCGR2A", "FCGR3A", "FGB", "FNBP1", "FOS", "FOSL1", "FOSL2", "FOXP3", "FRZB", "FUT2", "GAPDH", "GATA3", "GBP1", "GBP3", "GBP5", "GEM", "GINS1",
  "GJB2", "GJB6", "GLUL", "GOLIM4", "GPR35", "GPT", "GZMA", "GZMB", "GZMK", "HCAR3", "HERC6", "HHAT", "HIF1A", "HK2", "HLA-A", "HLA-B", "HLA-C",
  "HLA-DQB1", "HLA-DRB1", "HSPA5", "HSPA6", "HYAL4", "ICAM1", "ICOS", "IFI16", "IFI6", "IFIH1", "IFIT3", "IFNA1", "IFNG", "IFNGR1", "IFNLR1",
  "IGF2", "IGF2-AS", "IL10", "IL12B", "IL13", "IL15", "IL17A", "IL17F", "IL17RA", "IL18", "IL1A", "IL1B", "IL1F10", "IL1R1", "IL1RN", "IL2",
  "IL21", "IL21-AS1", "IL22", "IL23A", "IL23R", "IL2RA", "IL33", "IL36RN", "IL37", "IL4", "IL5", "IL6", "IL6R", "IL7", "INS", "INS-IGF2", "IRAK1",
  "IRS1", "ITGA2B", "ITGAL", "ITGAM", "ITGAX", "JAK2", "JAK3", "JDP2", "JRKL", "JUN", "JUNB", "JUND", "KANK4", "KDM5B", "KIR2DS1", "KIR3DL1",
  "KIR3DL2", "KLRB1", "LAMP1", "LAMP2", "LEP", "LILRA5", "LILRB2", "LINC01185", "LINC01250", "LMO7", "LPAL2", "LRRK2", "LTA", "LURAP1L",
  "LURAP1L-AS1", "LYZ", "MAF", "MBL2", "MCAM", "MCL1", "MEFV", "MICA", "MIR146A", "MIR21", "MIX23", "MMP1", "MMP3", "MMP7", "MMP9", "MRPS23",
  "MSN", "MTHFR", "MUCL1", "MX1", "MYC", "MYNN", "NABP1", "NAMPT", "NCOA7", "NDUFS1", "NFKB1", "NKG7", "NLRP3", "NMI", "NOD2", "NOS2",
  "NOXRED1", "NPEPPS", "NRG1", "NT5C3A", "OLR1", "OSMR", "PDCD1", "PDLIM7", "PER1", "PFDN4", "PFDN5", "PFKL", "PGD", "PGK1", "PHEX", "PI3",
  "PIK3CD", "PINK1", "PLA2G4D", "PLCG1", "PLG", "PLIN5", "PLS1", "PPARD", "PPARG", "PPARGC1A", "PPARGC1B", "PRDM1", "PRF1", "PRTN3", "PSG2",
  "PSMC2", "PSMD7", "PSME2", "PTGS1", "PTGS2", "PTH", "PTPN22", "PTX3", "PYGL", "RAC1", "RBM45", "REL", "RETN", "RGPD6", "RIT1", "RORC", "RPL15",
  "RPL36AL", "RPL41", "RPL7", "RPS19", "RPS21", "RPS26", "RPS6KB1", "RPS7", "RSAD2", "RUNX2", "RUNX3", "S100A12", "S100A8", "S100A9", "S100P",
  "SAA1", "SAMD9", "SAR1A", "SCN1A", "SEC14L2", "SEC24B", "SELL", "SERPINA1", "SERPINB1", "SERPINE1", "SF3B1", "SF3B3", "SGK1", "SH3BGRL3",
  "SIAH1", "SLC1A2", "SLC2A3", "SLC51B", "SLC7A11", "SLC7A5", "SMAD3", "SMARCA4", "SMOX", "SOCS1", "SOD2", "SOST", "SOX4", "SP7", "SPCS3",
  "SPON2", "SPP1", "SSR1", "STAT1", "STAT3", "STIM1", "SUOX", "SYT1", "TALDO1", "TBX21", "TEK", "TFPI", "TGFA", "TGFB1", "TGFBR3", "TIMP1",
  "TLR2", "TLR3", "TLR4", "TLR9", "TMBIM6", "TMEM45A", "TMPRSS11B", "TNF", "TNFAIP3", "TNFAIP6", "TNFAIP8", "TNFRSF10A", "TNFRSF1A",
  "TNFRSF1B", "TNFRSF9", "TNFSF10", "TNFSF11", "TNFSF13B", "TNFSF15", "TNIP1", "TOMM5", "TOMM7", "TPST2", "TPT1", "TRAF2", "TRAF3IP2", "TRAF4",
  "TRAF5", "TRBV20OR9-2", "TRIM22", "TRIM69", "TTC39B", "TYK2", "TYMP", "UBE2L3", "UQCR10", "UTP11", "VCAM1", "VDR", "VEGFA", "VIM", "WDR1",
  "WNK1", "WWOX", "XAF1", "XBP1", "YOD1", "YWHAB", "ZC3H12A", "ZFP36", "ZMIZ1", "ZNF316", "ZNF415", "ZNF483"
)

# Load the data.table package
library(data.table)

# Keep only the notes for the genes of interest.
 annot_filtered <- annot[annot$Symbol %in% genes_of_interest, ]
 
 # Filter the count matrix using GeneIDs as the key (MUCH MORE SECURE)
expr_data_filtered <- gset[rownames(gset) %in% annot_filtered$GeneID, ]
 
# Filter expression data for genes of interest
express <- rownames(expr_data_filtered)

# Mapping Entrez IDs to gene symbols
gene_symbols <- mapIds(org.Hs.eg.db, keys = rownames(expr_data_filtered), column = "SYMBOL", keytype = "ENTREZID", multiVals = "first")
## 'select()' returned 1:1 mapping between keys and columns
# Replace rownames with gene symbols
rownames(expr_data_filtered) <- gene_symbols

# View the updated dataframe
print("Data frame com rownames modificados para símbolos de genes:")
## [1] "Data frame com rownames modificados para símbolos de genes:"
print(expr_data_filtered)
##             GSM3308425 GSM3308426 GSM3308427 GSM3308428 GSM3308429 GSM3308430
## TNFRSF9            215        150         89        176        100        125
## ENO1              7327       8128       5485       6627       5161       7547
## PIK3CD            7748       6895       5701       5781       7085       7138
## PGD               8407       6039       3905       5438       5479       4306
## MTHFR              398        445        514        232        304        520
## TNFRSF1B         18991      14198      10710      13867      16404      12864
## PINK1              955        767        575        675        818        757
## IFNLR1              19         51         92         32         36         68
## RUNX3             1322       4550       5169       3042       2378       4679
## SH3BGRL3         11632      12131       9679      11733      10451      10061
## CD52              3566       5289       5744       4952       3982       5456
## IFI6              3133       1475        772       1568        809        730
## ZC3H12A            491        619        548        764        620        505
## UTP11              109        138        105        100         87        149
## JUN               1862       8233       8148       5007       5830      10406
## KANK4                1          0          0          0          0          0
## EFCAB7              12         32         42         26         19         41
## IL23R                0          0          9          0          1          4
## ADGRL2               0          0          2          0          0          0
## GBP3               112         99        152        225        123         97
## GBP1              4776       1250        708       1063        973       1330
## GBP5             16798       3645       2287       3083       2607       4404
## TGFBR3             108        964       1316        565        436        853
## VCAM1                0          1         10          0          2          2
## PTPN22             254        530        560        252        286        393
## CD160               12        238        246        119        139        158
## FCGR1A            4251       1170        436        941        512       1004
## MCL1             31572      23108      24285      23989      25605      23964
## CTSK                82         43         72         95         69         56
## RORC                23         20         78         13         30        139
## S100A9          174389     136992      72218     166968     160609      82813
## S100A12           4290       4083       2316       5337       3979       2054
## S100A8           70275      52729      28270      65639      65588      31098
## IL6R              5039       3544       2457       3368       4563       3440
## RIT1              1582       1320       1056       1503       1592       1205
## BGLAP                9          6          4         10          5         11
## IFI16             5627       3628       2121       2337       2596       3160
## AIM2               427        143        109         66        126        123
## CRP                  0          0          0          0          0          0
## FCGR2A           19096      14203       5545      10872      12557      11696
## HSPA6             3042       1929       1473       1952       2779       1769
## FCGR3A           27658      15736      17102      10001      19051      15848
## SELL             41683      31311      18369      30083      26582      28922
## GLUL             22808      15924      12630      18063      22910      13895
## PTGS2            17440       9183       3896       6214       7372      12501
## CRB1                 0          0          0          0          2          2
## KDM5B              434        347        379        444        452        367
## IL10                 5          7          4          4          4         11
## YOD1               242        325        442        291        283        240
## HHAT                17         41         54         16         35         56
## TRAF5              118        271        501        199        235        495
## NLRP3             1004       1092        606        566        522        898
## LINC01250            0          0          0          0          0          0
## RPS7              4213       8270      10963       9575       9055      10458
## RSAD2             2276        540        292        400        279        274
## FOSL2             3834       4660       4475       3545       4234       3851
## REL               1001        991       1067        670        679       1070
## TGFA               740        558        441        533        915        500
## DYSF              7777       4904       2078       4396       3539       3418
## HK2               1436        923        609       1000       1017        662
## CD8A               376       4290       2596       1188       1210       1667
## CD8B               242       1281       1170        684        552        577
## EIF5B              337        541        697        377        400        620
## IL1R1              164        285        211        241        234        190
## RGPD6               44         67         96         56         70         67
## IL1A                 1          1          0          0          0          0
## IL1B               929       1268        271        344        442        857
## IL37                 0          0          1          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             3426       3307       1562       2129       2788       1781
## NMI               3119        860       1191       1840       1856       1810
## TNFAIP6            777        489        319        294        482        321
## IFIH1              965        450        377        389        359        439
## SCN1A                0          0          0          0          0          0
## ABCB11               2          0          0          0          0          0
## RBM45               45         66         54         33         50         45
## FRZB                 0          1          1          0          0          0
## TFPI                 5          3          5          6          7          4
## STAT1            12808       5503       3057       5044       4313       5156
## NABP1             1002        778        474        533        659        692
## SF3B1             4388       4817       5085       3899       3730       4362
## CASP10             342        345        384        296        257        411
## CD28               147        383        915        397        623        814
## CTLA4               22         62        111         87         88         52
## ICOS                45        144        160         89        111        135
## NDUFS1             594        585        522        485        456        566
## CXCR2            25851      19265      13203      16164      19481      19491
## IRS1                25         50         79         23         41         42
## CCL20                2          3          3          1          0          4
## ATG16L1            209        368        488        358        264        360
## GPR35               82        161        142        191         85        102
## PDCD1               16         57         24         20         35         92
## PPARG                4          5          1          3          0          3
## RPL15             8125      13815      16171      13979      11672      16183
## EOMES               34        232        228        121        148        267
## CX3CR1            1228       1438        585        650        541       1451
## ACKR2                1          0          1          1          1          5
## CCR2               931       1139        394        183        230        775
## CCRL2               66         39         41         28         43         27
## TLR9                88         64         57         57         64         74
## ARHGEF3            663       1355       1445        880        906       1486
## ADAMTS9              0          0          0          0          0          0
## TMEM45A              0          0          1          4          1          2
## CD80                 2          5          5          4          4          2
## CD86              1198       1213        892        728        625        752
## MIX23               10         30         31         15         24         34
## PLS1                11          9         21          7         11         16
## PTX3                35         75         30         43         21         41
## GOLIM4             100        137         85         43         55        118
## MYNN               293        303        431        363        344        356
## TNFSF10           8062       3623       1996       2513       2958       3160
## ADIPOQ               0          0          0          0          0          0
## SPON2              130        587        365        623        410        936
## S100P             4031       1643       3078       4653       6224       3577
## WDR1              6832       6470       5499       5291       5797       6608
## CD38               189        252        208        216        188        428
## PPARGC1A             7         14          0          0          1          3
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          0          0          1          0
## CXCL8            14269      40868      27037      49181      62059      38786
## CXCL2               13          8          5          6          7         17
## AREG               124         37        148         55         17         56
## CXCL10              87         42         20         24          7         22
## CXCL13               0          0          0          0          0          0
## SPP1                52         35         65         27         82         33
## HERC6              198        187        196        142        138        201
## NFKB1             1056       1020        818        779        696        879
## SEC24B             497        429        509        412        358        458
## EGF                 31         32         32         23         34         22
## IL2                  0          0          0          0          1          1
## IL21                 0          1          3          1          1          0
## IL21-AS1             0          0          1          0          2          3
## SLC7A11              6          5          7         11          9          4
## IL15               112        132         92         65         55         90
## EDNRA                0          0          0          0          0          0
## TLR2              4647       3301       2210       2985       2499       3111
## FGB                  0          0          0          0          0          0
## DDX60             1097        378        366        318        255        450
## SPCS3             1900       2307       2088       1707       1813       2122
## TLR3                 3         17         14          5          5         20
## OSMR                28         24         30         27         15         20
## GZMK               132        757       1470        386        850       1341
## GZMA               243       2116       2025        924        992       1765
## ANKRD55             51         48         60         67         33         72
## CENPK               15         43        182         21         59        131
## CAST              2814       3256       2812       2159       2006       2532
## ERAP1             1792       1172       1192        995       1042       1443
## ERAP2             1388       1738        296       1112       1095       1712
## TNFAIP8            838       1146       1599        934       1268       1670
## CSF2                 0          0          0          0          0          3
## IL5                  0          0          0          1          1          2
## IL13                 0          1          0          0          0          2
## IL4                  2          0          4          0          0         13
## CD14              8936      11140       3631       5765       6288       6189
## CSNK1A1           2002       1771       1448       1549       1457       1763
## PPARGC1B           166        132        126        105         70        115
## TNIP1             5014       4601       4153       4274       4632       4277
## ATOX1              222        253        158        184        175        187
## FAXDC2             162        181        215        194        170        160
## IL12B                0          1          0          0          0          1
## MIR146A              0          0          0          0          0          0
## PDLIM7            2170       1996        932       2155       2278       1386
## SERPINB1          5640       5571       3193       5230       4743       4111
## SSR1              2456       2751       2145       1944       2072       2257
## CD83               539        424        411        348        272        596
## SOX4               175        296        192        277        192        226
## CMAHP               81         75        100         73         59         96
## HLA-A            63666      51852      38228      49718      39870      42463
## HLA-C            77198      64852      44225      64328      61196      91472
## HLA-B           144517     110030      75162     120772     105472     103482
## MICA               150        125        181        130        158        255
## LTA                 19         52         55         40         57         84
## TNF                124        396        145        212        146        130
## HLA-DRB1          4013       6062       2940       3633       2690       4398
## HLA-DQB1           421        730        511       3011        471        339
## PPARD              212        295        361        267        244        345
## CCND3             4059       4088       3609       4303       3339       4415
## VEGFA              221        199        170        171        208        184
## RUNX2              413        391        684        517        509        633
## IL17A                0          0          1          0          1          1
## IL17F                0          0          0          0          0          0
## PRDM1              552        686        861        425        358        772
## ATG5               362        471        486        444        423        414
## TRAF3IP2           112        197        224        191        157        233
## NCOA7              274        339        388        246        205        367
## SGK1              2736       2853       1787       1268       1734       2852
## IFNGR1            3696       2747       2280       3258       3068       2430
## TNFAIP3           2504       4237       7423       3954       2578       6491
## SOD2             55745      43148      31809      42424      48515      38883
## LPAL2               15         23         29          6         11         31
## PLG                  0          1          1          0          0          1
## CCR6                38         65        147         45         51        154
## RAC1              3199       2939       2654       3384       2948       3072
## ZNF316             741        871        612        867        643        735
## AHR                855       1037        911        790        551        830
## IL6                  7          1          9          4          5          4
## TOMM7             1236       2316       2599       1938       2415       2340
## CYCS               476        704        737        489        501        639
## AQP1                 1          1          5          3          3          3
## NT5C3A            1283        713        655        779        886        654
## EGFR                 0          0          0          0          0          0
## CD36              2569       3426       2019       2503       1700       1706
## SAMD9             2688       1475       1234       1144       1270       1829
## SERPINE1             9          5         11         10          2         10
## CUX1              1898       1678       1193       1393       1197       1367
## PSMC2              417        443        393        353        295        431
## NAMPT            64627      44963      31465      55150      59765      32702
## HYAL4                0          0          0          0          0          0
## LEP                  4          2          6          0         11          2
## CALD1               15         12         19         20         14         12
## BRAF               645        620        708        520        560        654
## EZH2                51         58         68         52         41         65
## DNAJB6            1668       1697       1420       1651       1658       1629
## CSMD1                3          2          5          2         22         15
## CTSB              5895       8342       4744       4399       3285       5854
## EGR3               561        535        152        133        226        525
## TNFRSF10A           79        144        186         92        144        203
## BNIP3L            3065       2541       1918       2502       2693       2158
## DUSP4               33         58         90         51         46         42
## NRG1                65         94        119         87         24         69
## RPL7              5539       9433      13219       9822       9278      11239
## IL7                 10         12         21          6         10          6
## GEM                  1          2          0          0          0          0
## MYC                248        470        615        272        349        571
## GPT                  1          1          4          2          0          3
## JAK2              1605       1207        885        837        726        871
## CD274              583        180        136        123        131        170
## IL33                 0          0          1          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              1          1          3          0          2          2
## TTC39B              43        102        246        107        123        169
## IFNA1                0          0          0          0          0          0
## TEK                  3         23          9         28         11         25
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              152        249        303        214        187        261
## ANXA1             7075       8806       8672       4819       5084       6858
## ERP44             1908       1627       1280       1471       1423       1442
## ZNF483               7         29         67         30         28         32
## TNFSF15             15         12          3          4          4          7
## TLR4              6050       6015       3130       3539       4990       4282
## PTGS1              656        761        808        899        883        645
## HSPA5             8341       6043       5967       6311       5315       7816
## FNBP1             3491       3751       3312       3027       2889       3946
## CARD9              230        240        122        201        175        212
## TRAF2               85        124        133        109        113        165
## CLIC3               37        171         93        113        150        184
## IL2RA               36        109        146         46        104        161
## GATA3              182        314        369        173        235        759
## VIM              17694      20339      14684      15966      15704      15250
## CREM               124        199        223        165        174        155
## DKK1                 0          0          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              950        913        931       1032       1008        864
## PRF1               633       4208       2491       2309       2032       5638
## ZMIZ1             2134       2089       1474       1646       1855       1951
## IFIT3            15574       3582       2244       5208       3603       3734
## TALDO1           13747       9895       6189      11167      11394       9044
## IGF2                 0          0          1          0          0          1
## INS-IGF2             0          0          1          0          0          1
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1              958       1425       1279       1070       1028       1400
## TRIM22            7247       3165       2129       2409       1823       2737
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          0          0          0          0
## SLC1A2               0          1          2          1          1          0
## FOSL1               27         71         31         25         14         24
## CCND1                9         14         13          9          5         10
## JRKL                56        106        119         34         51        131
## MMP7                 0          0          1          0          0          0
## MMP1                 1          2          0          0          3          1
## MMP3                 0          0          0          0          0          0
## CASP1             5164       3626       2507       3255       2716       2798
## DLAT               146        202        181        121        136        241
## IL18               140        117        109        131        110         91
## CD3E               819       3501       4859       2455       2525       4247
## MCAM               224        202        293        319        253        215
## WNK1              3515       3372       2894       2514       2523       4125
## TNFRSF1A          4776       4292       2064       2651       3211       3784
## GAPDH            18364      20325      14369      20383      17159      16477
## CD4               4852       5099       4702       3482       3019       5464
## SLC2A3           12157      11814       7369       9333       6787       7040
## CLEC4D             693        393        378        340        461        176
## KLRB1              197        870       1719        552        863       1018
## CD69              1250       2002       3406       1603       1551       3425
## CLEC2B            2659       2155       1565       2384       2491       1798
## OLR1                27         14          1          7          7          8
## ABCD2               37        133        200        106        136        194
## LRRK2            10976       6561       5864       7272       8997       5226
## VDR                494        373        359        325        432        343
## TMBIM6           13633      14761      11614      11271      12182      13938
## PFDN5             2700       3443       3998       3975       3085       3735
## SP7                  0          0          0          0          0          0
## MUCL1                0          0          0          0          0          0
## CD63              3912       3028       2583       3587       3023       2705
## SUOX              1367       1156       1038       1055       1168       1166
## RPS26              700       3521       8158       7028       6366       7913
## RPL41             4112       7190       9312       8336       7835       9293
## IL23A               25         33         56         41         43         54
## DDIT3              816        636        706        951        988        801
## IFNG                 5         95        131         57         30         60
## IL22                 0          0          0          0          0          1
## LYZ              86438      63027      51809     108771      71035      51896
## CAPS2                1          8          5          1          7          4
## SYT1                 1          5         14          2          1          1
## BTG1              9786       9904      14778      11213      11795      13904
## HCAR3             2829       2540       1410       1819       1654       2431
## GJB2                 1          1          1          1          2          2
## GJB6                22         33         22         15         39         20
## TNFSF11              1          0          7          0          2          3
## TPT1             33506      54642      66433      58762      56759      59660
## LMO7                17         37         83         48         37         97
## TNFSF13B          3009       2754       2092       2068       2321       1868
## LAMP1             3199       3480       2443       2702       2885       2961
## PSME2             2820       1839       1370       1939       1338       1642
## GZMB               311       1513       1456        975        646       1396
## RPL36AL           2060       2164       2157       2305       2305       2706
## PYGL              7954       5644       2643       5638       5824       4177
## HIF1A             2548       2451       1881       2918       3103       1667
## FOS              22296      46740      46884      50308      46684      40941
## JDP2               893        778        602        999        886        661
## NOXRED1              9         13         18          8          4         10
## SERPINA1         30483      27122      16661      28980      23113      17589
## CDC42BPB           239        307        209        167        139        257
## PLA2G4D              0          0          0          0          0          0
## TRIM69              20         21         21         11         21         25
## SLC51B               0          0          0          0          0          0
## SMAD3              373        618        880        478        467        712
## CYP1A1               2          1          0          1          0          0
## AKAP13            4672       4069       3682       2832       3057       3829
## MEFV              4464       2667       1996       2557       2558       2739
## SOCS1               87         70         61         45         55        112
## ATXN2L            1441       1989       2085       1503       1366       2323
## CD19                54         93        249         86        101        192
## ITGAL             5285       6069       5437       4464       3930       6665
## ITGAM             5837       5829       3620       4250       4439       4481
## ITGAX             6098       5958       4423       6019       5664       4730
## DNAJA2             817        636        650        653        615        806
## SIAH1               92        121        156        151        126        137
## ADCY7             2527       2890       2493       1475       1580       3002
## NOD2              2611       1020        727       1424       1387        443
## CMTM2             2942       2112       1344       2640       3024       2420
## SF3B3              691       1003        932        563        616       1247
## PSMD7              712        774        748        815        763        731
## WWOX                24         49         49         28         33         80
## MAF                263        692        582        263        358        623
## SLC7A5             119        318        260        211        284        368
## CXCL16            3836       1863       1634       1885       1956       2012
## XAF1              2581        992        974        715        676        992
## CD68              6129       5489       3499       4534       3340       4151
## PER1               622        602       1037       1246        572        688
## NOS2                 3          0          2          1          0          0
## TRAF4               42         97        138         82         91        147
## CCL2                 0          7         17          1          0          5
## CCL5               967       8243       8874       4226       3564       4951
## CCL3               238        338        268        173        178        507
## CCR7               107        381        522        380        424        715
## STAT3             7265       5104       3581       4240       4560       5042
## SOST                 0          0          0          0          0          0
## ITGA2B             414        365        360        753        699        256
## EFCAB13             11         15         45         16         12         13
## NPEPPS            1016        903        702        839        879        838
## TBX21               76        653        601        367        356        612
## COL1A1               3          0          0          1          4          0
## MRPS23             166        205        165        143        118        215
## MIR21                5          9          1          7          8          9
## RPS6KB1            263        361        427        247        301        373
## ACE                 25         28         61         21         26        106
## ERN1               830       1070       1420        682        903       1588
## PRTN3               40         13          1         29          2         17
## PLIN5              155        142         57        106        153        113
## RETN                83         68         44        131         59         47
## CCL25                0          0          0          1          1          0
## ICAM1             2565       2254       1197       1763       1775       1718
## TYK2              1892       2173       1624       1734       1868       1962
## SMARCA4            620        793        670        530        556        918
## ACP5               259        284        257        228        229        278
## JUNB             26574      50077      18954      54780      52521      32132
## CYP4F22             94         48         33         52         21         29
## JAK3              2057       2357       2028       2083       1943       2213
## JUND              4808       8639       5258       8393      10077       7967
## CEBPA             1241       1214        574       1091       1024        776
## CEBPG              263        317        356        321        245        334
## ACP7                 0          0          0          0          2          7
## ZFP36            18624      32508      17164      31390      29263      22637
## TGFB1             6072       7008       3890       5572       5253       5468
## RPS19             5643       9974      12585      10710      10270      12916
## PSG2                 0          0          0          0          0          0
## FUT2                 1          1          9          4          4          1
## NKG7               804       6553       5829       4062       3155       5383
## ZNF415               3          2          9          4          3         17
## LILRB2            7068       5564       3714       4917       4793       4073
## LILRA5            4604       3943       1474       3242       3981       2642
## KIR3DL1             31         61         53         28         52         75
## KIR3DL2              6         32        102         63         31        151
## SMOX                92        111        135        147        118        123
## BMP2                 3          7          3          5          0          5
## GINS1                2          8         10          3          6          6
## PLCG1              220        749       1047        408        470       1031
## YWHAB             6224       7104       5424       5476       5783       6340
## PI3               3948       1928        292       1311        156        579
## MMP9              4194       2848        667       3176       4200       1463
## CD40               334        247        137        131        125        182
## PFDN4               30         62         75         46         45         55
## BMP7                 0          0          0          0          0          0
## RPS21             2176       4277       5294       5211       5025       6179
## MX1               3252       1337       1153        836        776        808
## PFKL              1220       1377        938        968        834       1347
## IL17RA            7894       5359       3566       4887       5020       4533
## UBE2L3            1131       1179       1084       1007        902       1159
## TPST2             1023       1545       1300       1184       1017       1408
## XBP1               940       1234       1336       1152       1133       1254
## UQCR10             550        647        581        549        555        614
## SEC14L2             11         20         41         28         19         36
## APOL6             4173       1696       1351       1213       1218       1954
## APOL1             2322        834        510        725        799        783
## TYMP              7482       4155       2260       4360       3942       2634
## BEND2               39         42        109         59         37         49
## PHEX                11          5         20          4          6         10
## TIMP1             1392       1803       1480       1068       1239       1909
## FOXP3               42         69         75         52         76         77
## MSN              30304      25333      20651      21752      20890      26501
## PGK1              9900       8842       7120       7263       6756       7591
## LAMP2             8221       6466       5529       6588       8014       6131
## CD40LG              51        153        253        110        141        298
## IRAK1             1332       1730       1456       1265       1208       1599
## COX2             39992      63303      80860      61595      46396      56578
##             GSM3308431 GSM3308432 GSM3308433 GSM3308434 GSM3308435 GSM3308436
## TNFRSF9            101        166        150        104         51        131
## ENO1              6629       5839       6206       6010       5729       5522
## PIK3CD            6976       6348       7702       4977       5417       4844
## PGD               4600       6740       5903       4435       4610       4058
## MTHFR              564        389        518        325        393        356
## TNFRSF1B         15464      14056      13732      11344      12920      10709
## PINK1              788        899        941        540        747        440
## IFNLR1              63         38         66         36         16         48
## RUNX3             4118       3755       2697       3697       3916       4408
## SH3BGRL3         10348      11997       9956      10343      11600       9212
## CD52              4626       2991       4278       5631       4359       4253
## IFI6               786       1952        637       1824        736        508
## ZC3H12A            693        649        453        877        931        995
## UTP11              120        101        116         96         79         83
## JUN               6838       3488       6866       6561       7894      10311
## KANK4                1          0          0          1          0          0
## EFCAB7              46         20         23         17         18         19
## IL23R                2          3          0          0          2          4
## ADGRL2               0          0          0          0          0          0
## GBP3               140        282        274         68        138         53
## GBP1               784       1612       1066        557        286        274
## GBP5              2472       4959       2426       2235       1469       1040
## TGFBR3             763        746        401        716        679       1048
## VCAM1                1          7          5          2          0          5
## PTPN22             435        341        398        281        211        316
## CD160              185        143        101         94         64        119
## FCGR1A             356       1095        480        503        212        221
## MCL1             24197      28918      28200      28445      27742      18408
## CTSK                75         43        107        114         48         61
## RORC                50         13         52          3         29         32
## S100A9          102836     152151     119272     117422     112214      89816
## S100A12           2196       3795       3050       2968       2851       2919
## S100A8           38048      57591      45633      43499      40319      35386
## IL6R              3780       4370       4678       2168       2761       2580
## RIT1              1224       1557       1317       1843       2188       1125
## BGLAP                8          7         11          4          6          5
## IFI16             2416       3110       2286       1475       1138       1235
## AIM2                77        133        145         77         62         60
## CRP                  0          0          0          0          0          0
## FCGR2A           11960      12686      11761       8604       8778       7547
## HSPA6             2166       2633       1651       1090       1203       1184
## FCGR3A           16626      18954      16955      13357      12839       7845
## SELL             20647      36638      22564      25233      26124      17290
## GLUL             16203      16555      16667      15936      17411      13566
## PTGS2             3227       7759      14738       2393       2136       2222
## CRB1                 4          1          2          0          2          1
## KDM5B              400        418        439        404        489        313
## IL10                 1          1          6          9          1          3
## YOD1               359        274        280        434        452        413
## HHAT                50         34         34         36         40         45
## TRAF5              428        221        319        187        255        200
## NLRP3              601       1003        974       1319        905        693
## LINC01250            1          0          0          0          0          1
## RPS7             10714       7513       7126       8961       9520       8473
## RSAD2              252        860        191        446        123         62
## FOSL2             4114       4425       3971       4120       4396       5376
## REL               1015        680        886       1158       1141        833
## TGFA               652        466        549        336        418        500
## DYSF              2632       5472       3552       2570       2732       2431
## HK2                846        906       1179        811        662        631
## CD8A              1954       2449        955       1563       1166       2337
## CD8B               865       1094        461        698        436        501
## EIF5B              535        364        524        310        325        337
## IL1R1              199        215        301        243        305        201
## RGPD6               98         62         66         62         60         46
## IL1A                 0          0          1          0          0          0
## IL1B               332        550        497        227        254        515
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             2087       2030       1913       1794       1788       3204
## NMI               1532       1716       1493        996        897        740
## TNFAIP6            365        627        223        180        131        178
## IFIH1              390        499        261        300        241        206
## SCN1A                0          0          0          0          0          0
## ABCB11               2          2          1          1          3          0
## RBM45               62         46         49         54         34         35
## FRZB                 0          0          1          0          1          0
## TFPI                 3          8          2          7         12          3
## STAT1             3429       5941       3804       2945       2175       1710
## NABP1              628        666        817        402        469        451
## SF3B1             4811       4217       5263       4215       4661       3772
## CASP10             359        252        413        271        294        254
## CD28               764        339        590        471        623        426
## CTLA4               93         42         71         86         94         78
## ICOS               141        106        112        114         98         96
## NDUFS1             501        477        552        373        424        346
## CXCR2            17011      20829      17760       8991      10545       8457
## IRS1                82         29         91         23         32         55
## CCL20                2          1          1          1          2          3
## ATG16L1            395        281        298        332        348        321
## GPR35              130         93        143        167        291        196
## PDCD1               40         35         30         18         23         30
## PPARG                1          5          0         12          3          5
## RPL15            15321      11640      12182      13420      14096      11956
## EOMES              178        204        114         92         86        156
## CX3CR1             657        736       1042        252        181        554
## ACKR2                1          3          2          1          3          1
## CCR2               354        483        523        218        178        226
## CCRL2               27         61         40         42         29         26
## TLR9                57         68        123         47         57         64
## ARHGEF3           1263        926        882        836        931        927
## ADAMTS9              0          1          0          0          0          0
## TMEM45A              5          2          1          5          1          1
## CD80                 8          3         14          3          5          5
## CD86               781        909        896        640        582        480
## MIX23               31         20         30         23         21         14
## PLS1                10         16         18          7         14          9
## PTX3                36         84         57         79         70         55
## GOLIM4              75         98         95         57         60         71
## MYNN               307        269        366        359        403        298
## TNFSF10           2596       4064       2958       1562       1444       1064
## ADIPOQ               0          0          0          0          0          0
## SPON2              661        333        523        589        278       1191
## S100P             3546       2784       5359       3731       2223       1712
## WDR1              6084       6371       6357       4631       5057       4616
## CD38               258        130        459        185        124        240
## PPARGC1A             5          3          8          0         12          1
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          0          0          0          2
## CXCL8            30976      25086      35808      32430      58462      32299
## CXCL2                3         18         10          7         16          8
## AREG                21         82         27        315        228        104
## CXCL10              11         36         35          5          3          6
## CXCL13               0          0          0          0          0          0
## SPP1                62        121         30         38         80        104
## HERC6              139        223        174         98        160         90
## NFKB1              774        786        779        785        726        614
## SEC24B             482        397        466        422        569        370
## EGF                 45         42         16         37         51         18
## IL2                  0          0          0          1          1          1
## IL21                 0          0          0          0          0          1
## IL21-AS1             1          0          1          0          0          0
## SLC7A11             10          6         12         10         18          4
## IL15                77         83         80         65         46         39
## EDNRA                1          0          0          0          0          0
## TLR2              2469       3594       3201       3108       4051       1955
## FGB                  0          0          0          0          0          0
## DDX60              269        420        278        284        167        156
## SPCS3             1757       1932       2295       1529       1598       1582
## TLR3                13          4         10          4          9         18
## OSMR                26         27         24         32         39         24
## GZMK              1157       1618        621        482        579        545
## GZMA              1305       1430        835        867        792       1344
## ANKRD55             38         39         85         60         35         44
## CENPK               67         88         95         10         56         68
## CAST              2700       2587       2238       2609       2944       1867
## ERAP1             1335       1036       1187       1666       1497        761
## ERAP2             1524       2459       2503       1168       1009        130
## TNFAIP8           1502        972       1278        913        900        890
## CSF2                 0          1          0          1          0          0
## IL5                  0          1          0          0          1          0
## IL13                 1          1          0          0          2          0
## IL4                  5          2          0          7          0          1
## CD14              5911       6682       8226       5243       4547       5879
## CSNK1A1           1363       1585       1628       1303       1269        984
## PPARGC1B           153         75        107        193        150         99
## TNIP1             4863       4998       4771       3528       4253       4346
## ATOX1              172        204        180        199        198        245
## FAXDC2             229        176        150        133        251        129
## IL12B                0          2          1          0          1          1
## MIR146A              0          0          1          0          1          1
## PDLIM7            1944       2158       2260       1582       2079       1769
## SERPINB1          4102       4014       3331       3827       3672       3311
## SSR1              2170       2392       2544       1861       2034       1600
## CD83               301        551        622        752        443        485
## SOX4               267        107        155        242        396        227
## CMAHP              103         63         72         63         65         61
## HLA-A            39142      59096      53261      51438      32838      33649
## HLA-C            52883      67491      83964      96432      50281      53391
## HLA-B            97682     112829     112485     107813      83425      77180
## MICA               211        121        109         88        101         91
## LTA                 62         38         42         38         49         35
## TNF                189        198        287        324        345        358
## HLA-DRB1          3522       3228       4888       3216       2731       3505
## HLA-DQB1           582        459       3847        496        496        594
## PPARD              345        231        263        232        274        245
## CCND3             3959       4472       3502       4961       5302       3453
## VEGFA              243        210        238        229        245        148
## RUNX2              507        462        539        453        785        497
## IL17A                0          0          1          0          0          0
## IL17F                0          0          0          0          0          0
## PRDM1              452        723        515        748        840        523
## ATG5               410        366        392        347        387        360
## TRAF3IP2           209        129        198        143        154        145
## NCOA7              255        449        337        259        280        216
## SGK1              1797       3312       3282       1862       2298       1597
## IFNGR1            2303       2674       2501       2458       3082       2243
## TNFAIP3           2968       3271       2108       7772       7770       5175
## SOD2             35021      44744      33172      28542      32003      27013
## LPAL2               27         11         11         13         15         19
## PLG                  1          0          0          1          0          2
## CCR6                79         38         90         30        105         95
## RAC1              2683       3380       2915       2769       2863       2318
## ZNF316            1011        798        727        960        984        890
## AHR                672        854        838       1424       1223        655
## IL6                  5          1          1          9          5          2
## TOMM7             2682       1692       2015       2251       2158       2208
## CYCS               516        545        605        546        456        505
## AQP1                 6          2          2          2          4          2
## NT5C3A             748        785        655        513        605        473
## EGFR                 0          0          0          0          0          0
## CD36              1880       2292       1957       2704       2250        902
## SAMD9             1344       1658       1529        645        568        560
## SERPINE1             6         13          5          8          8          8
## CUX1              1271       1374       1481       1504       1655       1115
## PSMC2              354        331        348        390        332        300
## NAMPT            41624      50520      37491      45618      54141      32282
## HYAL4                0          0          0          0          1          0
## LEP                  7          0         10          1          0          2
## CALD1               26         14         13          8         28         16
## BRAF               654        538        610        598        629        398
## EZH2                66         42         84         51         45         58
## DNAJB6            1418       1702       1650       1634       1948       1200
## CSMD1               34          3          0          1          2          6
## CTSB              4263       6730       6198       4995       6425       4389
## EGR3               210        640       2164        143        213        206
## TNFRSF10A          207         91        134        136        100        112
## BNIP3L            2115       2320       2466       2003       2413       1725
## DUSP4               48         32         39        112         58         55
## NRG1                34        114         52         70         83        146
## RPL7             11502       8154       9142       8933       9979       8202
## IL7                 17         20         13          4          4          9
## GEM                  0          1          0          0          1          2
## MYC                598        666        549        396        320        199
## GPT                  1          2          3          2          4          3
## JAK2               821        807        834        869        748        649
## CD274              102        181        102         73         54         57
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              1          5          0          2          4          1
## TTC39B             215        100        129        128        127        105
## IFNA1                0          0          0          0          0          0
## TEK                 21         20         17          7         18         23
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              189        191        203        216        194        215
## ANXA1             6388       8511       5529       6977       6482       5730
## ERP44             1472       1403       1418       1272       1207        997
## ZNF483              42         28         28         38         31         28
## TNFSF15              8          2         12          0          0          4
## TLR4              3353       4013       4559       2093       2161       2441
## PTGS1             1372        847        560        691       1501        638
## HSPA5             5489       5258       6857       5022       4940       5444
## FNBP1             3626       3519       3592       2711       2980       2742
## CARD9              215        173        255        157        181        190
## TRAF2              134         94        126        110        111         99
## CLIC3              255         74        106         94        124        132
## IL2RA              125         47         79         81         45         69
## GATA3              439        271        297        249        346        253
## VIM              17449      21735      16181      14920      17459      15025
## CREM               193        149        163        192        202        182
## DKK1                 0          0          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              873        808        810        954       1130        797
## PRF1              3276       2027       2499       1731       1161       2970
## ZMIZ1             1901       2280       1811       2061       2489       1835
## IFIT3             2535       6148       2276       2907       1254        655
## TALDO1            8838      11437      10159       6978       8671       6566
## IGF2                 0          0          0          0          0          0
## INS-IGF2             0          0          0          0          0          0
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1378       1088       1366       1077       1142       1117
## TRIM22            1822       2747       1852       1845       1292       1206
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          0          0          0          0
## SLC1A2               3          0          2          1          1          3
## FOSL1               17        173        100        113         54         52
## CCND1                5          4          5          2          5          5
## JRKL               105         61         91         35         38         40
## MMP7                 0          0          0          0          0          0
## MMP1                 5          0          0          1          4          1
## MMP3                 0          0          0          0          0          0
## CASP1             2618       3113       2870       2226       1927       2079
## DLAT               207        164        184        136        106        130
## IL18               118         94        101        168        108        104
## CD3E              3628       2810       2315       2201       2748       2565
## MCAM               222        194        239        229        242        167
## WNK1              3102       3598       4043       2371       2545       2205
## TNFRSF1A          2921       3766       2927       1481       1767       1763
## GAPDH            18555      21105      20679      18573      18995      16457
## CD4               4455       3739       3823       3737       3400       3043
## SLC2A3            4323       9149      11461       7363       8193       8858
## CLEC4D             241        481        273        408        215        250
## KLRB1             1110        499        963        837        936        684
## CD69              1467       1681       1284       2356       2239       1797
## CLEC2B            1882       2374       1929       1567       1715       1025
## OLR1                 9         41          7          5         11          1
## ABCD2              176        105        102         83         96         89
## LRRK2             8254       8085       9732       5427       7310       4903
## VDR                380        476        417        271        370        221
## TMBIM6           12521      13597      14128       9071      10697       9857
## PFDN5             3783       3320       3207       3614       3429       3063
## SP7                  0          0          0          0          0          0
## MUCL1                1          0          0          0          0          0
## CD63              2586       3887       2781       3677       3805       2687
## SUOX              1044       1078       1213        731        854        765
## RPS26             7342       3166       3207        854        804        699
## RPL41             8866       6705       6932       7573       7217       7622
## IL23A               39         25         42         24         25         24
## DDIT3              827       1056        747        901       1153        643
## IFNG                32         41         24         21         34         37
## IL22                 0          0          1          0          1          1
## LYZ              82127      85154      42990     123617      96761      84499
## CAPS2                6          3          6          6          7          5
## SYT1                 4          2          7          0          3          4
## BTG1              9977      11289      10127      12981      14883       8918
## HCAR3             1350       1805       2117       1041       1359       1259
## GJB2                 0          1          8          0          2          1
## GJB6                16         39         48         51         31         36
## TNFSF11              2          1          1          5          0          0
## TPT1             65408      47294      47666      53395      73565      47265
## LMO7                75         55         60         37         49         40
## TNFSF13B          1811       2164       1639       1475       1242       1083
## LAMP1             2751       2923       3127       2378       2585       2165
## PSME2             1477       1780       1327       1579        956       1055
## GZMB               962        731        711        835        515       1301
## RPL36AL           2564       2415       2077       2228       2125       2001
## PYGL              4161       5502       5108       3962       4334       3371
## HIF1A             2140       2306       1982       3903       3857       2776
## FOS              35343      18666      55848      34775      39344      34967
## JDP2               836        949        922       1151       1167        827
## NOXRED1              9          4          9          5          7          2
## SERPINA1         20513      25645      15552      22153      24374      19074
## CDC42BPB           254        142        203        197        203        252
## PLA2G4D              0          0          0          0          0          0
## TRIM69              22          8         16         10         13         14
## SLC51B               0          0          0          0          0          0
## SMAD3              684        512        471        627        673        499
## CYP1A1               1          0          0          0          0          0
## AKAP13            3540       3587       4341       3645       3603       3007
## MEFV              2539       3168       2484       1771       1881       1694
## SOCS1               55         97         55        109         76         64
## ATXN2L            2240       1718       1755       1513       1643       1560
## CD19               190         45        156         92         49        102
## ITGAL             5856       5573       4872       5138       4998       5365
## ITGAM             4574       5464       5263       4383       4060       4574
## ITGAX             6362       5751       5668       5385       7010       5109
## DNAJA2             642        670        670        687        806        502
## SIAH1              114        115        128        162        144        135
## ADCY7             2628       2034       2430       1825       1755       1865
## NOD2              1363        480        821        464        469        329
## CMTM2             1860       2452       3301       1714       2234       1720
## SF3B3              890        670        854        464        482        580
## PSMD7              747        708        746        905        898        638
## WWOX                59         32         41         43         54         38
## MAF                540        407        393        313        283        460
## SLC7A5             346        248        304        523        799        392
## CXCL16            1442       2415       2056       2301       2591       1993
## XAF1               957       1321        588        594        369        432
## CD68              4100       4766       4030       5438       4802       3217
## PER1               617        972        558       3251       3687       1198
## NOS2                 1          0          0          0          2          2
## TRAF4              154         92        122        134        120        132
## CCL2                 1         22         15          7          0          3
## CCL5              5166       5789       2498       3479       4137       5158
## CCL3               176         86        223         90        152        249
## CCR7               646        320        499        268        326        241
## STAT3             4375       5047       4504       3078       3670       2859
## SOST                 0          0          0          0          0          0
## ITGA2B            1268        668        230        360       1132        430
## EFCAB13             31         23         18         26         19         17
## NPEPPS             974       1002       1153        682        707        583
## TBX21              577        477        433        298        340        592
## COL1A1               0          0          1          0          3          0
## MRPS23             169        174        200        125        140        120
## MIR21                4          9          4          9         11          4
## RPS6KB1            369        294        314        246        314        215
## ACE                 49         46         40         28         50         30
## ERN1              1118       1070       1254        947       1437        962
## PRTN3               10         29          5         16          9         16
## PLIN5               83        112        123        100         87        134
## RETN                78        109         45         98        113         71
## CCL25                0          0          0          1          0          0
## ICAM1             1554       2427       1666       2440       1999       1840
## TYK2              2156       2023       2532       1346       1639       1734
## SMARCA4            809        625        720        560        675        567
## ACP5               314        200        278        191        393        162
## JUNB             43937      34632      46114      44625      54433      53440
## CYP4F22             21         53        103         26         79         18
## JAK3              2285       1766       1798       1751       1538       1687
## JUND              9184       7564       8097       9073       9258       9244
## CEBPA             1076        715        872       1393       1355        944
## CEBPG              286        258        302        376        398        285
## ACP7                 1          3          0          0          0          0
## ZFP36            24555      23923      30893      28726      35749      36442
## TGFB1             6754       7221       5726       6570       7041       6071
## RPS19            12618       8475       9337       9935      10739       8922
## PSG2                 0          0          0          0          0          0
## FUT2                 3          3          2          1          3          3
## NKG7              4546       4406       2782       3983       3107       5457
## ZNF415               5          7          8          0         15          4
## LILRB2            4562       4872       4890       4501       3998       3756
## LILRA5            2950       3242       2048       3000       1503       2922
## KIR3DL1             89         37        115         86        163          2
## KIR3DL2             52         45         42         72         44         40
## SMOX               173        132        101        103        212        131
## BMP2                 3          9         27          5          4          1
## GINS1                5          4          8          7          6          7
## PLCG1             1014        601        720        524        565        610
## YWHAB             5646       5706       6365       4769       5057       5366
## PI3                198       1310        462        692        484        433
## MMP9              2728       5279       3958       1506       2596       2547
## CD40               162        126        134        114         66        109
## PFDN4               43         40         41         53         43         62
## BMP7                 0          0          0          0          0          0
## RPS21             5735       4032       4357       4640       4740       4489
## MX1                875       1967        449       1153        456        423
## PFKL              1368        897       1235        966       1089        958
## IL17RA            4904       6010       5857       4430       4797       3788
## UBE2L3            1008       1066        996        818        874        763
## TPST2             1356       1348       1262       1208       1115       1350
## XBP1              1372        875       1214       1146       1062        989
## UQCR10             591        542        610        540        446        506
## SEC14L2             43         30         18         29         38         20
## APOL6             1261       1764       1275       1113        811        875
## APOL1              736       1038        720        370        306        348
## TYMP              4119       6005       3664       3981       4012       2773
## BEND2               80         40         24         51        136         37
## PHEX                12          3         10         13          7          9
## TIMP1             1188       2346       1264       1596       1573       1126
## FOXP3               68         40         73         40         50         35
## MSN              24123      26117      23743      20648      23508      19058
## PGK1              7233       7822       7441       7460       7524       6392
## LAMP2             6286       7291       7121       4953       6002       4160
## CD40LG             174        134        180        111        151        102
## IRAK1             1779       1497       1806       1849       1726       1640
## COX2             58938      48093      52101      59809      57247      53089
##             GSM3308437 GSM3308438 GSM3308439 GSM3308440 GSM3308441 GSM3308442
## TNFRSF9             56        281        141        175        132        185
## ENO1              4923       6091       5444       7114       7361       5566
## PIK3CD            2765       7917       7447       7727       7559       5956
## PGD               2629       8544       4894       7199       5436       3916
## MTHFR              365        328        422        277        691        351
## TNFRSF1B          7984      15137      12857      12853      15958      14463
## PINK1              268       1013        759        971        901        714
## IFNLR1              60         12         79         43         91         73
## RUNX3             5154       2250       3378       2209       5034       5005
## SH3BGRL3          6216      11108       9709      10201      12548      10289
## CD52              3729       2351       4022       4632       6073       5150
## IFI6              2099       1728        758       1357        750        915
## ZC3H12A            556        569        491        556        547        590
## UTP11               87        111        103        116         98        103
## JUN               5433       2527       3117       4387      23735       1084
## KANK4                5          0          0          0          0          0
## EFCAB7              23         25         42         20         28         29
## IL23R                3          0          6          3          3          5
## ADGRL2              14          0          0          0          0          1
## GBP3               187        313        283        117        314        192
## GBP1              1028       1570        960        808        620        394
## GBP5              2916       3154       3431        954       2042       1244
## TGFBR3            1425        403        679        352       1127       1074
## VCAM1               26          1          3          0          2          4
## PTPN22             312        382        508        379        426        485
## CD160              176         24         74         84        125         58
## FCGR1A             230       1224        456        754        383        331
## MCL1             17214      28958      25812      23374      24315      30010
## CTSK                61         61         80         56         85         74
## RORC                36         12         69         36         34         61
## S100A9           53018     183796      98212     204593      98291     104071
## S100A12           1397       5787       3124       7757       3299       2257
## S100A8           20928      66703      36312      81933      34596      38474
## IL6R              1297       5140       4595       4003       4668       3897
## RIT1               951       1604       1248       1493       1043       1242
## BGLAP                3         10         11          7          6          7
## IFI16             1904       3123       2627       3222       1829       2700
## AIM2                61        140         99        150         70         63
## CRP                  3          0          0          0          0          0
## FCGR2A            4599      13139      11555      16028      10611      12181
## HSPA6              688       2340       2048       3189       1420       1320
## FCGR3A           14166      21212      15324      16735      14743      14035
## SELL             11914      42366      26385      34119      28601      26363
## GLUL              8440      16472      13074      16238      12875      17454
## PTGS2             1976       6281       7613       4968      12795       7467
## CRB1                10          0          0          1          1          3
## KDM5B              277        519        474        401        423        428
## IL10                 8          6          0          3          1          5
## YOD1               353        358        456        260        183        291
## HHAT                39         27         41         23         36         36
## TRAF5              294        128        501        273        439        347
## NLRP3              876        903        579        859        964        865
## LINC01250            1          0          0          0          1          0
## RPS7              7039       5987       8152       8756       9627      10653
## RSAD2             2907        877        279        374        205        159
## FOSL2             4202       5056       3816       3766       3547       4681
## REL               1162        935       1293        746       1066        896
## TGFA               234        440        581        642        474        408
## DYSF              1686       7305       3990       5296       3568       3513
## HK2                514       1711       1079        938       1000        733
## CD8A              1751       1447       1860        888       2826       2779
## CD8B               688        356        477        522       1268        810
## EIF5B              396        334        601        392        532        447
## IL1R1              114        329        271        327        185        406
## RGPD6               75         51        103         58         77         77
## IL1A                 4          0          0          2          1          0
## IL1B               266        425        321       1641        842        292
## IL37                 5          0          0          0          0          0
## IL36RN               3          0          0          0          0          0
## IL1F10               2          0          0          0          0          0
## IL1RN             1444       2187       1882       4428       2034       2415
## NMI                904       2431       1341       2082       1054       1333
## TNFAIP6            220        429        466        503        219        827
## IFIH1              502        470        403        381        309        327
## SCN1A               23          0          0          0          0          0
## ABCB11              15          1          0          1          2          0
## RBM45               52         33         76         30         57         38
## FRZB                 2          0          0          0          0          0
## TFPI                 9          3          6          3          7          1
## STAT1             3224       5595       4138       3659       3019       2193
## NABP1              337        711        820        749        511        635
## SF3B1             4080       4841       5548       3984       4048       4936
## CASP10             333        338        382        259        464        356
## CD28               568        189        676        480        606        472
## CTLA4              120         49        106         79         30        116
## ICOS               138         51        216        159        165        178
## NDUFS1             393        499        545        389        509        515
## CXCR2             5731      18676      18566      19453      17748      22622
## IRS1                36         13         89         42         97         44
## CCL20                3          0          1          2          3          3
## ATG16L1            351        248        372        267        374        384
## GPR35              128        175        106        123        125        125
## PDCD1               30         24         29         22         46         31
## PPARG               11         14          3          4         14          2
## RPL15             9401       9530      12659      12474      16730      15250
## EOMES              207         80        109         62        302        181
## CX3CR1             658        868        955       1101       2019        689
## ACKR2               10          2          2          0          0          2
## CCR2               207        544        667        613        891        494
## CCRL2               37         31         30         23         30         19
## TLR9                32         63        100         75         73         45
## ARHGEF3           1062        788       1125        840       1206        992
## ADAMTS9             12          0          0          0          0          1
## TMEM45A              8          4          2          6          0          0
## CD80                 4          5          9          2          4          9
## CD86               650       1218        713        634       1194        880
## MIX23               15         13         23         27         27         29
## PLS1                20          7         15         11         30         20
## PTX3                78         62         52         86         50          8
## GOLIM4              56         88        101         55        123         84
## MYNN               373        355        325        290        367        358
## TNFSF10           1525       3917       2870       3934       2549       2692
## ADIPOQ               5          0          0          0          0          0
## SPON2              805        145        462        287        628        582
## S100P             1524       3327       3162       2847       2810       1561
## WDR1              3728       6978       5863       6522       5985       5370
## CD38               397        174        374        178        279        139
## PPARGC1A            22          2          1          2          6         10
## TMPRSS11B            3          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  3          0          1          0          0          1
## CXCL8            11591      14955      22229      16980      47195      12713
## CXCL2               17         18          3          6         33          4
## AREG               195         93         27         22         20        140
## CXCL10              41         23         16         21         21          1
## CXCL13               1          2          0          0          0          1
## SPP1                17         62        113         26         48         90
## HERC6              287        164        177        256        167        178
## NFKB1              719        729        944       1007        807        910
## SEC24B             359        515        531        415        447        555
## EGF                 24         29         25         18         20         12
## IL2                  4          0          2          2          0          5
## IL21                 2          0          0          0          0          2
## IL21-AS1             6          1          3          1          0          0
## SLC7A11             13         10         13          8         10         10
## IL15                56         91         63         49        104         99
## EDNRA                7          0          0          0          0          0
## TLR2              2041       3478       3514       2879       2498       3750
## FGB                  5          0          0          0          0          0
## DDX60              791        382        324        297        285        260
## SPCS3             1330       1864       1949       1812       1781       2041
## TLR3                15          5         12          3         18         19
## OSMR                32         28         49         22         19         26
## GZMK               768        326        753        354       1138        533
## GZMA              1640        751       1005        581       2192       1223
## ANKRD55             29         81        122        106         65         23
## CENPK               80         11        140        110         53        124
## CAST              2042       4155       3152       2502       3496       2832
## ERAP1             1228       1849       1580        924       1973       1222
## ERAP2             1420        171       1598        146       1668        201
## TNFAIP8            859       1010       1647       1257       1271       1288
## CSF2                 0          0          0          2          0          2
## IL5                  3          0          3          0          1          0
## IL13                 3          0          0          0          0          0
## IL4                  2          4          8          4          9          1
## CD14              3334       7188       5266       8222       9686       7144
## CSNK1A1            931       1817       1733       1564       1593       1565
## PPARGC1B           165        156        133         82        178         71
## TNIP1             2857       5286       4404       6048       4412       4070
## ATOX1              105        206        154        161        209        184
## FAXDC2             134        133        178        111        192        110
## IL12B                7          0          0          0          0          0
## MIR146A              0          0          0          0          0          0
## PDLIM7             577       2596       1675       2156       1736       1648
## SERPINB1          2559       4934       3706       6307       4010       4906
## SSR1              1493       2446       2422       2132       2382       2190
## CD83               491        271        272        221        611        374
## SOX4               124        249        232        147        157        120
## CMAHP              103         45        104         65        102         81
## HLA-A            33819      58020      38549      37633      40095      36373
## HLA-C            47620     126512      95391      81409      59363      88108
## HLA-B            69256     132999     124957      93415      94895      99189
## MICA               106         88        164        130        264        137
## LTA                 43         25         63         57         73         35
## TNF                252        254        198        168        194         99
## HLA-DRB1          5050       5653       6527       3718       6850       3349
## HLA-DQB1          3747       4545       3323        659        950        903
## PPARD              195        243        415        285        370        359
## CCND3             3439       5244       3514       4179       4547       5360
## VEGFA              177        277        166        222        198        303
## RUNX2              428        440        623        451        348        879
## IL17A                2          0          0          0          0          0
## IL17F                3          0          0          0          0          0
## PRDM1              746        412        688        510        411       1248
## ATG5               361        399        441        389        347        454
## TRAF3IP2           130        116        185        186        178        226
## NCOA7              381        301        304        304        376        337
## SGK1              1706       2080       2256       2635       4011       1276
## IFNGR1            1433       3404       3130       3571       2529       3241
## TNFAIP3           6091       2606       2709       2330       4316       5724
## SOD2             12639      43231      35934      42482      27510      42433
## LPAL2               27          7         22         15         35         18
## PLG                 13          0          0          0          0          0
## CCR6                87         16        105         72         57        117
## RAC1              1568       3154       2868       2921       2737       3379
## ZNF316             334        862        831        866        696        766
## AHR                935        666        865        566       1237        794
## IL6                 10          1          4          3          5          2
## TOMM7             1693       1650       2279       1964       2184       2485
## CYCS               667        419        558        522        686        529
## AQP1                 1          3          1          3          2          0
## NT5C3A             511        981        778        942        692        734
## EGFR                24          0          0          0          0          0
## CD36              2207       2776       2343       2185       2593       1356
## SAMD9             1333       1551       1600       1363       1511       1307
## SERPINE1             7         10         17          2         21          5
## CUX1               999       1939       1536       1179       1936       1145
## PSMC2              356        310        366        316        384        374
## NAMPT            21743      47631      38500      62539      28326      55021
## HYAL4                5          0          0          0          0          0
## LEP                  4          1          6          0          4          2
## CALD1               17         10         28          2          5          2
## BRAF               440        790        800        638        643        771
## EZH2                78         36         91         50         74         65
## DNAJB6             995       1628       1678       2000       1346       1574
## CSMD1               38          0          1          3          0          2
## CTSB              5693       5838       4541       5600       6759       5872
## EGR3               224        162        150        204        662        180
## TNFRSF10A          121         97        239        165        149        127
## BNIP3L            1170       3122       2093       2299       2007       2164
## DUSP4              137         26         57         64         42        157
## NRG1                49        127         49        218        154        136
## RPL7              6387       6080       9748       8789      10058      11335
## IL7                 14         13         31          8         11         25
## GEM                  4          0          3          1          2          0
## MYC                204        266        602        960        365        577
## GPT                  6          2          4          1          3          1
## JAK2               668       1677        980        965       1115        640
## CD274               94        113        178        160         64         98
## IL33                13          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              4          1          6          1          3          0
## TTC39B             145        116        250         97        202        130
## IFNA1                2          0          0          0          0          0
## TEK                 17         15         62         43          5          8
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              178        163        188        185        221        243
## ANXA1             5799       5779       5582       6371       7686      10395
## ERP44              928       1661       1320       1361       1437       1242
## ZNF483              47         18         48         25         29         21
## TNFSF15              8         13          9         10          9          1
## TLR4              1665       6188       2443       4343       5121       5763
## PTGS1              379        711        717        480        963        452
## HSPA5             4284       4856       5128       6280       5741       5137
## FNBP1             2316       3467       4011       3533       3720       3699
## CARD9               94        212        175        139        285        130
## TRAF2               96         88        160         96        155         95
## CLIC3               92         30         95         62        175        105
## IL2RA              108         51        132        148         91        151
## GATA3              321        131        341        397        480        539
## VIM              10419      18909      12897      22381      19048      18529
## CREM               273        115        177        163        107        283
## DKK1                 3          0          0          0          0          0
## MBL2                 5          0          0          0          0          0
## SAR1A              777        885        851        755        704        781
## PRF1              3841       1297       2500       1119       2469       2534
## ZMIZ1             1235       2269       2246       1352       3028       2243
## IFIT3             7701       5132       2881       3749       1624       1756
## TALDO1            3265      11814       8570      11474       8760       8569
## IGF2                 3          0          0          0          0          0
## INS-IGF2             3          0          0          0          0          0
## IGF2-AS              2          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1061       1252       1348       1189       1518       1168
## TRIM22            2880       3186       2156       2030       1611       1661
## PTH                  1          0          0          0          0          0
## SAA1                 2          0          1          0          0          0
## SLC1A2              24          1          1          0          5          0
## FOSL1               76         51         15         52         28         36
## CCND1                8          5          5          4          6          3
## JRKL                45         60         98         38         93         71
## MMP7                 2          0          0          0          0          0
## MMP1                 3          1          2          2          0          1
## MMP3                 3          0          0          0          0          0
## CASP1             1862       3951       2535       2944       2577       2895
## DLAT               168        154        192        161        249        198
## IL18                63        139        102        113        130         81
## CD3E              2509       1579       3422       2759       4050       3680
## MCAM               165        310        299        253        246        210
## WNK1              2139       3490       4348       2557       4519       3637
## TNFRSF1A          1011       3338       3705       3727       4082       2918
## GAPDH            13322      20989      13791      20838      19931      17347
## CD4               2884       3784       3678       4169       4934       3240
## SLC2A3            3476      10019       8524      13580       7168       9516
## CLEC4D             321       1079        185        878        356        355
## KLRB1              883        197        708        635        799        780
## CD69              2693        826       1260       1618       2043       2040
## CLEC2B            1157       2059       1329       2404       1346       1538
## OLR1                11         11         16         66          2          9
## ABCD2              132         64        238        113        175        126
## LRRK2             3707      11541       8528       7689       6570       7067
## VDR                285        454        404        476        467        326
## TMBIM6            6876      14303      13117      12811      14589      13198
## PFDN5             2744       3150       3155       3164       3448       4017
## SP7                  2          0          0          0          0          0
## MUCL1                1          0          0          0          0          0
## CD63              2127       4186       2453       3606       3109       3573
## SUOX               568       1193       1131       1182       1138       1145
## RPS26             2718        705        694       3135       4185        815
## RPL41             5851       5036       6872       7389       8218       8781
## IL23A               22         15         33         23         29         32
## DDIT3              506        957        620        846        615        746
## IFNG                68         19         31         27        106          7
## IL22                 2          2          0          1          0          1
## LYZ              53655      87349      35621     116350      47676     118507
## CAPS2               15          3          3          5          5          2
## SYT1                 4          3          3          1         11          3
## BTG1              8905      12080       9496      10602       9468      12552
## HCAR3              528       1070       1476       3320       1580       1051
## GJB2                 2          9          0          3          1          1
## GJB6                 9         92         22         32         13         19
## TNFSF11              3          0          0          3          3          2
## TPT1             32490      41368      50160      60578      57563      63436
## LMO7                53         30         98         55         69         41
## TNFSF13B          1518       2285       1895       2667       1674       2967
## LAMP1             1826       2922       2692       2545       3116       2697
## PSME2             1451       1820       1355       1222       1422        876
## GZMB              2078        609        822        482       1122       1904
## RPL36AL           1591       2034       2356       2274       2466       2583
## PYGL              1307       7971       3794       7545       4023       4650
## HIF1A             2187       2543       2039       2179       1589       2254
## FOS              15403      47157      25985      34691      74159      12952
## JDP2               491       1215        834        980        822       1180
## NOXRED1              9         11         10          7          7          7
## SERPINA1         13309      26390      25903      26305      19232      22240
## CDC42BPB           146        182        265        159        343        197
## PLA2G4D              9          0          0          0          0          0
## TRIM69              23         10         16         15         10         15
## SLC51B               2          0          0          0          0          0
## SMAD3              622        416        621        483        767        578
## CYP1A1               5          2          1          3          1          1
## AKAP13            3317       4293       3972       2830       4103       4032
## MEFV              1108       3706       2922       3060       2909       3062
## SOCS1               23         46         57         73         87         58
## ATXN2L            1170       1565       2000       1556       2372       1802
## CD19                67         20        192        112        134        161
## ITGAL             5764       6014       5561       4413       7071       4926
## ITGAM             2826       6723       4613       5423       6130       5116
## ITGAX             2514       6980       5970       6526       5411       5930
## DNAJA2             464        810        689        668        672        790
## SIAH1              127        132        172         97         96        133
## ADCY7             1802       2643       2684       1777       3628       2656
## NOD2               434       1234        826        926        518        440
## CMTM2              708       2984       2385       3240       1504       1781
## SF3B3              637        616        904        734       1093        700
## PSMD7              720        789        651        702        694        760
## WWOX                43         33         48         47         56         39
## MAF                441        272        607        372        532        480
## SLC7A5             372        173        219        135        235        381
## CXCL16            1067       2640       1318       2053       1885       3313
## XAF1              1867       1409        968        671        685        677
## CD68              3840       5446       3561       3785       4926       3754
## PER1              1312       1104        656        351        637       1727
## NOS2                11          1          1          0          3          0
## TRAF4              108         47        134         73        134        103
## CCL2                16          1          4          6         19          5
## CCL5              6625       2716       3542       2073       6779       5328
## CCL3               341        157         92         95        391         49
## CCR7               193        152        987        493        655        343
## STAT3             2263       5627       4979       4801       3743       4747
## SOST                 2          0          0          0          0          0
## ITGA2B             236        400        510        271        383        128
## EFCAB13             26         12         41         15         12         26
## NPEPPS             477       1210        966       1007        899        945
## TBX21              578        201        446        204        591        568
## COL1A1              12          3          2          1          0          0
## MRPS23             149        151        188        185        147        190
## MIR21                2         11          6          4          3          5
## RPS6KB1            275        267        434        345        396        409
## ACE                 49         18         45         41         62         66
## ERN1               737       1095       1273        840       1388       1990
## PRTN3                9         21          3         27          7         10
## PLIN5               51        125        108        180         80        124
## RETN                37        109         49        162        101         83
## CCL25                3          2          1          0          1          0
## ICAM1             1264       1818       1194       1590       1375       1170
## TYK2               987       2387       2261       1791       2110       1952
## SMARCA4            473        574        814        596        912        665
## ACP5               222        307        354        312        579        221
## JUNB             11973      36103      27082      69331      27132      16330
## CYP4F22             16         28         28         46         37          6
## JAK3              1191       1693       2282       2079       1545       1871
## JUND              3004       4575       4827       6333      13900       5709
## CEBPA              559       1494       1034       1171        981        631
## CEBPG              287        293        276        286        292        302
## ACP7                10          0          0          2          2          0
## ZFP36            13394      26302      15591      48473      25928       8984
## TGFB1             2695       5935       4784       5824       6167       4534
## RPS19             7440       5985       9508       9684      11406      11133
## PSG2                 4          0          0          0          0          0
## FUT2                 7          0          4          1          3          1
## NKG7              6802       2507       3034       2375       6380       5434
## ZNF415              11          6          8         16         15          7
## LILRB2            3453       6582       4908       4898       4897       4438
## LILRA5            2001       5400       2844       4145       2932       2661
## KIR3DL1            146         11         55         23         91        289
## KIR3DL2            145         18         26         41         28         66
## SMOX                72         85        118         70        150         65
## BMP2                 3          8          4         12          4         12
## GINS1               15          4          9          8          7         10
## PLCG1              663        335       1068        582        988        661
## YWHAB             4054       7361       5755       6023       6069       5103
## PI3                147       1768        683       1504        951        444
## MMP9               240       8338       1685       4703       2338       1219
## CD40               141         71        203        147        145        112
## PFDN4               61         31         52         43         34         55
## BMP7                 5          0          0          0          0          0
## RPS21             3131       2803       4609       4485       4947       5372
## MX1               1728       1546        965       1329        732       1259
## PFKL               658       1025       1167       1011       1526       1194
## IL17RA            1853       7514       5531       5383       5338       4896
## UBE2L3             756       1104       1022       1004       1156       1054
## TPST2             1018       1104       1314       1104       1787       1264
## XBP1               976        794       1137       1080       1005       1239
## UQCR10             380        608        562        536        636        568
## SEC14L2             18         19         46         30         42         21
## APOL6             1709       1498       1716        942       1123        832
## APOL1              404        834        757        502        622        406
## TYMP              2356       4757       3385       4088       3641       2554
## BEND2               28         58         51         26         51         19
## PHEX                29          4         29          4         11         16
## TIMP1             1147       2180       1041       1505       1924       2198
## FOXP3               77         32         87         54         95         92
## MSN              15577      28501      23537      22925      28237      22201
## PGK1              5391       8888       7006       9001       7795       7335
## LAMP2             2846       8642       7117       7069       5850       6385
## CD40LG             102         59        207        166        169        192
## IRAK1             1039       1574       1642       1507       1961       1704
## COX2             40808      32486      43141      47537      68415      48921
##             GSM3308443 GSM3308444 GSM3308445 GSM3308446 GSM3308447 GSM3308448
## TNFRSF9             89        110         76        205        155         18
## ENO1              6388       5838       7148       6613       6882       2125
## PIK3CD            6047       6453       6022       6198       6502       2641
## PGD               4299       4762       5385       5830       4844       1687
## MTHFR              404        451        455        280        395        129
## TNFRSF1B         13726      13272      13292      15217      16715       4731
## PINK1              675        654        695        858        695        237
## IFNLR1              67         46         34         60         58         11
## RUNX3             5689       3061       4882       4369       4341        941
## SH3BGRL3          9597       9560      13230      13773      13168       4361
## CD52              4748       3841       3960       5492       4979       2274
## IFI6               597       1835       1271       1468       1035        227
## ZC3H12A            563        457        855        739        790        146
## UTP11              113         95        113        103        114         17
## JUN               1578       7170       6433       8679       9152       1798
## KANK4                1          0          0          0          0          0
## EFCAB7              21         28         28         17         31          7
## IL23R                0          2          0          1          7          1
## ADGRL2               0          0          0          0          0          0
## GBP3               220        207        195        203        192         63
## GBP1               449        597        436        589        490        106
## GBP5              2150       2352       1478       1611       2140        216
## TGFBR3            1034        520        703        904        862        123
## VCAM1                1          5          4          4          1          0
## PTPN22             385        388        343        361        345         79
## CD160              142         88        232        121        132         26
## FCGR1A             349        430        399        453        475         79
## MCL1             24519      21995      24552      21580      24402       3764
## CTSK                72         80         80         61         45         18
## RORC                34         37         25         26         57         30
## S100A9           75498     113153     116100     143716     139545      38998
## S100A12           2815       4254       3124       4969       3730        934
## S100A8           25950      42740      39429      54411      54618      20094
## IL6R              3201       3642       2723       3481       3372       1423
## RIT1              1316       1437       1589       1303       1476        251
## BGLAP                5          5         10          9          8          7
## IFI16             1572       2681       1528       2212       2150        394
## AIM2                29         72         46         86         97         25
## CRP                  0          0          0          0          0          1
## FCGR2A            7483      11092       9501      10336      12320       1952
## HSPA6             1199       1251       1188       1928       1662        559
## FCGR3A           11591       8457      12475      14033      15829       2435
## SELL             22826      31752      27342      40278      29349       6076
## GLUL             12012      17941      15873      17482      17637       3610
## PTGS2              806       5585       3574       6828       3796        167
## CRB1                 1          0          1          0          2          0
## KDM5B              454        409        457        364        392        105
## IL10                 7          3          0         10          5          0
## YOD1               531        319        423        220        333         41
## HHAT                62         35         28         25         57          7
## TRAF5              401        341        260        175        339        165
## NLRP3              935        829       1299        719        834        162
## LINC01250            0          0          0          0          0          0
## RPS7              9616       6607      10835       8237      10543       3786
## RSAD2              118        973        219        392        253         32
## FOSL2             5016       4446       6078       4644       4938        487
## REL               1310       1158       1124        627        858        175
## TGFA               391        447        530        419        544         54
## DYSF              2500       3776       2502       3792       3652        951
## HK2                890        967        936       1089        729        166
## CD8A              2145       1554       1180       2761       2390        642
## CD8B               916        839        510       1227       1024        533
## EIF5B              545        421        428        424        432        617
## IL1R1              216        248        245        222        329         48
## RGPD6              110         60         70         46         74         42
## IL1A                 1          0          0          0          0          0
## IL1B                55        289        412        330        369         47
## IL37                 1          1          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN              979       2156       2141       2976       2632       1011
## NMI                889       1350       1003       1583       1312        230
## TNFAIP6            185        397        220        505        559        109
## IFIH1              325        375        308        320        331         48
## SCN1A                0          0          0          0          0          0
## ABCB11               0          0          0          0          0          0
## RBM45               45         56         48         44         49         10
## FRZB                 0          0          0          0          0          0
## TFPI                 3          1          2          4          3          6
## STAT1             3437       3525       3055       3105       3363        600
## NABP1              382        683        417        487        594         96
## SF3B1             4482       4658       4649       3695       4428        905
## CASP10             384        314        324        262        277        109
## CD28              1169        618        716        351        613        263
## CTLA4              197         80         98         84         80         32
## ICOS               246        121        168         88        149         55
## NDUFS1             557        461        493        470        490        127
## CXCR2            11280      17627      11707      16244      16173       2143
## IRS1                44         67         40         19         33         29
## CCL20                0          1          0          3          5          0
## ATG16L1            549        348        413        350        384        132
## GPR35              203        142        168        152        154         70
## PDCD1               70         29         33         65         21          6
## PPARG                4          1          4          5          3          0
## RPL15            15247      12037      17297      12327      15527       5675
## EOMES              215         94         89        226        111         33
## CX3CR1             410        684        302        732        457        125
## ACKR2                0          0          2          0          3          2
## CCR2               415        312        387        439        235        148
## CCRL2               35         38         43         41         35          9
## TLR9                50         77         57         49         61         31
## ARHGEF3           1441       1090       1140       1127       1136        283
## ADAMTS9              0          0          0          0          0          0
## TMEM45A              1          2          1          2          3          4
## CD80                 8          7          6          1          6          0
## CD86               823        852       1014        887        861        214
## MIX23               25         23         24         16         16         17
## PLS1                25         17         18         10         21          6
## PTX3                28         58         99         41         38          9
## GOLIM4              92         64        105         72         59         22
## MYNN               353        275        406        320        402         66
## TNFSF10           1639       2277       1403       2195       1944        328
## ADIPOQ               0          0          0          0          0          0
## SPON2              520        574        989        842        552         49
## S100P              131       3625       4006       5603       4442        161
## WDR1              5355       5049       5425       6046       5419       1630
## CD38               240        292        277        149        209         38
## PPARGC1A             6         14          5          3          8          1
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          1          0          0          0          0
## CXCL8             4876      41735      64868      43159      27905       2948
## CXCL2                1          5         21          8         11          0
## AREG               284         26         90         72         67          4
## CXCL10               9         14         17         20         15          1
## CXCL13               0          0          0          2          0          0
## SPP1                57        145         54         17          4          3
## HERC6              148        238        259        160        190         72
## NFKB1             1155        828        897        746        809        286
## SEC24B             654        473        513        372        407        158
## EGF                 30         19         29         19         25          9
## IL2                  3          0          3          2          0          0
## IL21                 0          0          0          0          1          0
## IL21-AS1             0          1          1          0          0          0
## SLC7A11              6          9         12          7          6          2
## IL15                56         59         63         76         74         26
## EDNRA                0          0          0          0          0          0
## TLR2              2963       2301       2131       2835       2327        438
## FGB                  0          0          0          0          0          0
## DDX60              261        395        253        345        241         63
## SPCS3             2078       1511       1592       1931       1997        468
## TLR3                 7         11          5          8         12          0
## OSMR                35         30         31         19         20          2
## GZMK              1290        747        557        913        749        166
## GZMA              1160        690       1230       2045       1213        197
## ANKRD55            111         37        102         41         62         48
## CENPK              122         98         21         39         69          5
## CAST              2755       3039       3101       2805       2307        585
## ERAP1             1453       1577       1879       1123       1117        260
## ERAP2             1883       1186       1392       1040       2530       1083
## TNFAIP8           1441       1226       1113        952       1185        511
## CSF2                 0          0          0          0          0          0
## IL5                  0          0          0          0          0          0
## IL13                 1          0          1          0          0          1
## IL4                  2          1          6          0          7          4
## CD14              6376       5947       8166       9455       8430       3254
## CSNK1A1           1424       1379       1349       1585       1382        574
## PPARGC1B           159         99        131         92        111         18
## TNIP1             3916       4515       4453       4794       5219       1552
## ATOX1              187        154        179        247        165        131
## FAXDC2             183        155        175        159        133         85
## IL12B                1          0          0          0          0          0
## MIR146A              0          0          0          0          0          0
## PDLIM7            1246       1770       1613       2194       2068        599
## SERPINB1          2911       4643       3867       4331       5136       1406
## SSR1              2349       2213       2261       2167       2332        450
## CD83               331        316        637        349        404        143
## SOX4               196        291        338        249        206        179
## CMAHP              100         65         70         63         86         38
## HLA-A            50273      35150      50187      53123      55509      18332
## HLA-C            82242      86630      77811      73045      76808      15075
## HLA-B           102024      85207     110902     109018     100757      27745
## MICA               104        134        143        113        132         68
## LTA                 49         57         51         35         50         32
## TNF                149        229        278        221        228        118
## HLA-DRB1          8402       3579       5568       6344       5188        957
## HLA-DQB1          3816        269       1714       1480        416        199
## PPARD              486        335        402        254        322        169
## CCND3             6591       3483       4060       4398       4106       1358
## VEGFA              188        193        279        205        214         12
## RUNX2              635        543        630        505        526         99
## IL17A                0          0          0          0          0          0
## IL17F                0          0          1          0          0          0
## PRDM1             1435        391        521        632        508        111
## ATG5               555        396        468        455        473        138
## TRAF3IP2           218        219        181        111        198         59
## NCOA7              364        271        302        217        311        119
## SGK1               995       1779       4580       1423       1921        254
## IFNGR1            3120       2704       2471       2932       2587        513
## TNFAIP3           9198       2576       5582       4987       4762        439
## SOD2             25772      37038      37619      41494      41172       7874
## LPAL2               17         11         16         15         18          2
## PLG                  0          1          1          0          0          0
## CCR6               159         72         47         67         72         31
## RAC1              2920       2266       3050       3881       3252       1498
## ZNF316             811        819        838        614       1025        478
## AHR               1188        784       1299        841        749        197
## IL6                  2          1          2          1          6          1
## TOMM7             2613       2028       1973       1572       2790       1222
## CYCS               601        487        560        599        595        133
## AQP1                 5          1          2          5          5          0
## NT5C3A             633        602        567        785        621        313
## EGFR                 0          0          0          0          0          0
## CD36              2002       1826       2873       2567       2009        452
## SAMD9              875       1368        770       1124        976        166
## SERPINE1             4          8         12         12          2          3
## CUX1              1357       1446       1700       1332       1563        397
## PSMC2              431        322        378        384        342         89
## NAMPT            33090      44660      43585      52984      49331       5815
## HYAL4                0          0          1          1          0          0
## LEP                  0          4          0          3          3          0
## CALD1               13         19          7         19         14          3
## BRAF               637        654        588        534        579        143
## EZH2                69         45         62         50         68         29
## DNAJB6            1828       1423       1861       1575       1689        518
## CSMD1                2          4          2          0          2          8
## CTSB              6465       5365       5988       5741       5745       1371
## EGR3                28        209        124        311        226         37
## TNFRSF10A          245        220        167        109        126         50
## BNIP3L            2086       1942       2300       2448       2157        461
## DUSP4              276         91        158         79         76         17
## NRG1                30         35        240         27         73         12
## RPL7             11952       9631      12324       8618      11556       6141
## IL7                  8         11         11         10         11          8
## GEM                  3          0          2          0          3          0
## MYC                583        417        473        190        510        354
## GPT                  0          1          1          3          7          1
## JAK2               879        833        808        685        831        183
## CD274               82         98         73         75        106         12
## IL33                 0          0          0          0          0          1
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              0          1          2          2          1          2
## TTC39B             289        195        172        113        160         94
## IFNA1                0          0          0          0          0          0
## TEK                  5          4         46         40          3         15
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              209        177        247        235        242         78
## ANXA1             6777       5312       8239       7822       6583       1291
## ERP44             1231       1170       1330       1480       1462        335
## ZNF483              45         52         37         23         38         10
## TNFSF15              1          7          6          2          4          3
## TLR4              2166       3647       1929       4367       3301        761
## PTGS1              909        751        989        643        729        230
## HSPA5             5643       4532       6215       7099       6047       1165
## FNBP1             3451       3632       3393       3292       3550        962
## CARD9              176        168        177        221        185         65
## TRAF2              152        114        150        120        120         83
## CLIC3              110        139        156        128        148         49
## IL2RA              129        105        132         60         93         46
## GATA3              496        303        461        209        513        167
## VIM              15064      15559      17316      20522      19225       4926
## CREM               312        183        284        221        207         52
## DKK1                 0          0          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A             1189        776       1138        948        953        319
## PRF1              2706       1925       2566       3477       2339        302
## ZMIZ1             2400       1988       2493       2038       2354        273
## IFIT3             1112       4452       2021       3746       1910        292
## TALDO1            6766       8364       9312      10485       9895       3119
## IGF2                 0          0          0          0          0          1
## INS-IGF2             0          0          0          0          0          1
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1488       1158       1309       1203       1290        351
## TRIM22            1597       2273       1759       1973       1606        407
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          1          0          0          0
## SLC1A2               2          1          4          4          4          0
## FOSL1                8         32         77         36         53          2
## CCND1                6          5          5          9          7          2
## JRKL                66         83         43         46         44         22
## MMP7                 0          0          0          0          0          0
## MMP1                 1          0          1          0          0          0
## MMP3                 0          0          0          0          0          0
## CASP1             2282       2209       2553       2736       2567        649
## DLAT               171        156        183        164        173         40
## IL18               102         91        100        110        111         20
## CD3E              3950       2603       3011       3225       3791       1400
## MCAM               274        226        249        349        221         73
## WNK1              3623       3431       2670       2854       2648        509
## TNFRSF1A          1937       2912       2378       2887       2752        929
## GAPDH            16511      16308      18451      20742      18011       6618
## CD4               4970       4194       5187       4206       3946        939
## SLC2A3            6879       8989      11735      11064      10840       1605
## CLEC4D             282        321        171        384        278         88
## KLRB1              579        754        793        829       1482        244
## CD69              2205       1332       2166       2214       2198        152
## CLEC2B            1154       1388       1754       2141       1843        561
## OLR1                 4          3          7         12          4          0
## ABCD2              198        141        163         98        159         91
## LRRK2             5250       7250       5160       6591       5152        679
## VDR                298        438        192        337        347         85
## TMBIM6           10987      11146      11896      12720      12535       2707
## PFDN5             3457       2993       4540       3744       4020       2279
## SP7                  0          0          1          1          0          0
## MUCL1                0          0          0          0          0          0
## CD63              3052       2432       3575       3903       3376       1024
## SUOX               967        974        935       1162       1039        286
## RPS26             3989       3150       4434       3683       4384        423
## RPL41             7794       6331       9553       7003       9350       3817
## IL23A               42         41         31         26         48         34
## DDIT3              495        756        913        927        846        270
## IFNG                 7         26         20        144         35          1
## IL22                 0          0          0          0          1          0
## LYZ              82162      77797     122045      51530      41655      15415
## CAPS2                6          5          4          6          4          1
## SYT1                 4          1          0          0          2          1
## BTG1             14369       9551      13082      12777      11302       2817
## HCAR3              694       1163       1113       1275       1520        318
## GJB2                 0          1          7          2          4          0
## GJB6                28         14         40         39         50         11
## TNFSF11             10          4          4          2          4          2
## TPT1             59325      47023      66046      50353      66883      20924
## LMO7                84         81         51         30         52         42
## TNFSF13B          1135       2546       1862       1740       2246        537
## LAMP1             2808       2488       2894       2922       3160        876
## PSME2             1507       1083       1591       1445       1571        410
## GZMB               828        693       1429       1716       1066        124
## RPL36AL           2945       1853       2953       2562       3005       1015
## PYGL              3041       4367       4106       5541       4540       1030
## HIF1A             3529       2544       4196       2657       2517        443
## FOS               7685      44038      41457      56001      46903       6362
## JDP2              1161        852       1000       1045       1073        168
## NOXRED1              3          8          8          6         13          1
## SERPINA1         18766      22005      24615      24077      30959       5794
## CDC42BPB           295        209        188        157        260         51
## PLA2G4D              1          0          0          0          0          0
## TRIM69              13         18          9         10         12         12
## SLC51B               0          0          0          0          0          0
## SMAD3              995        612        797        529        663        238
## CYP1A1               0          0          2          1          0          0
## AKAP13            5178       3035       4110       2999       2799        842
## MEFV              1760       2846       2210       2869       2508        495
## SOCS1               85         51         97         54         90         32
## ATXN2L            1858       1892       1892       1653       1824        514
## CD19                64        117         65         44         71        127
## ITGAL             5788       4512       5594       5089       5402       1716
## ITGAM             4444       4466       5132       5069       4645       1173
## ITGAX             4337       6028       6049       5992       6446       1040
## DNAJA2             741        606        781        639        663        200
## SIAH1              217        133        182        150        113         37
## ADCY7             2359       2512       1994       1962       2148        429
## NOD2               551       1126       1071        439        902        102
## CMTM2             1064       2350       1893       2539       2732        536
## SF3B3              785        792        736        728        672        315
## PSMD7              941        693        980        823        888        334
## WWOX                53         35         51         45         37         20
## MAF                496        425        447        457        506        147
## SLC7A5             768        315        472        320        482         42
## CXCL16            1880       2421       2433       2798       3037        319
## XAF1               519        860        531        835        827        151
## CD68              4461       3999       5339       5260       4352        855
## PER1              3863        709       1870       1331       1046        398
## NOS2                 5          0          3          3          2          0
## TRAF4               98        133        149         55        123         55
## CCL2                 2          3         10          9          4          0
## CCL5              4962       2557       4294       7944       5621       1530
## CCL3                34        160        201        284        163         65
## CCR7              1094        631        563        168        447        663
## STAT3             3920       4441       3567       4322       3913       1005
## SOST                 0          0          0          0          0          0
## ITGA2B             604        254        499        332        295        133
## EFCAB13             17         33         24          9         10          5
## NPEPPS             838        847        729        957        776        178
## TBX21              457        328        460        724        585         50
## COL1A1               1          2          2          0          4          1
## MRPS23             198        135        186        147        170         53
## MIR21                5          7          6          7          7          1
## RPS6KB1            438        297        310        295        301        117
## ACE                117         53         52         32         61         24
## ERN1              1928       1021       1268       1131       1466        300
## PRTN3                2          6          9         15         12         44
## PLIN5               72        116         78         77        125         54
## RETN                50        104         85         75         96        136
## CCL25                0          1          2          0          0          0
## ICAM1             1365       1802       2408       1622       2746        293
## TYK2              1628       1868       1715       1795       1867        664
## SMARCA4            753        686        778        579        655        468
## ACP5               329        186        442        272        402        164
## JUNB             15185      43478      40710      41202      56317       6655
## CYP4F22             28         23         32         25         21          4
## JAK3              1890       1879       1717       1440       2553       1606
## JUND              4835       7293       9571       8371       9836       3938
## CEBPA              962        906       1227       1104       1078        292
## CEBPG              348        258        372        299        299         80
## ACP7                 0          1          0          0          0          0
## ZFP36             8870      23332      30000      23815      33685       2151
## TGFB1             5995       5502       6598       6351       7121       1509
## RPS19            11404       9087      11256       9069      11812       8142
## PSG2                 0          0          0          0          0          0
## FUT2                 1          2          4          2          4          4
## NKG7              3700       2747       4655       7222       4843        696
## ZNF415               3          3          8          1          3          0
## LILRB2            4069       4769       4512       4190       5216        825
## LILRA5            1285       2886       2500       3060       2541       1363
## KIR3DL1             60        105         61         69        218          6
## KIR3DL2            157         71        122         52         83          7
## SMOX               122        123        146        120        122        111
## BMP2                 5          4          7          2          3          3
## GINS1                5         13          8          8          7          1
## PLCG1             1077        776        688        411        731        403
## YWHAB             5480       4799       6280       6363       5808       2125
## PI3                605        306        933       1674        740        741
## MMP9              1055       1927        783       3435       1633        904
## CD40               140        173        120        142        184         61
## PFDN4               56         43         63         62         72         28
## BMP7                 0          0          0          0          0          0
## RPS21             4979       4053       5783       4178       5836       2895
## MX1                432       1824        914       1665        767        169
## PFKL              1187       1211       1191       1024       1132        509
## IL17RA            5112       4555       3907       4909       4612       1260
## UBE2L3             951        884       1098       1214       1024        355
## TPST2             1394       1184       1318       1549       1310        298
## XBP1              1789        924       1306       1411       1581        303
## UQCR10             541        482        625        550        594        268
## SEC14L2             56         38         47         13         77         28
## APOL6             1404       1130       1150        931        793        295
## APOL1              468        467        515        508        574        117
## TYMP              2848       4202       4733       4531       5269       2666
## BEND2               51         57         44         60         60         24
## PHEX                 6         12          8          5          7          0
## TIMP1             1713       2160       1838       1844       2427        736
## FOXP3              119        100        110         39         64         25
## MSN              23284      23371      23149      25434      25291       4407
## PGK1              6926       7260       8103       7559       8456       1428
## LAMP2             5543       6015       5828       6937       6483        999
## CD40LG             348        132        148        127        200         63
## IRAK1             1978       1494       1708       1412       1738        375
## COX2             64192      50557      68548      49585      68176     618605
##             GSM3308449 GSM3308450 GSM3308451 GSM3308452 GSM3308453 GSM3308454
## TNFRSF9             27         53        115         58        128         78
## ENO1              1357       7300       6575       4805       6118       5685
## PIK3CD            2009       4433       6326       4731       7073       4864
## PGD               1327       4080       4807       5566       4553       3454
## MTHFR              105        490        519        332        640        403
## TNFRSF1B          3177      10040      14510       9137      14386      11891
## PINK1              250        383        782        483        686        616
## IFNLR1              12         33         39         31         55         66
## RUNX3              757       3336       3790       3052       3779       4778
## SH3BGRL3          4222       8038       9290       9045      10097       9312
## CD52              1141       4531       3633       4650       4499       5156
## IFI6               348        889       1167       1820       2029       3452
## ZC3H12A             76        573        709        611        650        655
## UTP11               21         97         77         38         63         76
## JUN               3323      13631      10703      11634      27441      23029
## KANK4                0          0          0          0          0          0
## EFCAB7               4         27         36         13         27         19
## IL23R                0          4          2          2          7          0
## ADGRL2               0          0          0          0          0          0
## GBP3                30        442        232         69        451         73
## GBP1               114       1853        939        362       1917        881
## GBP5               280       6204       3030       1644       5461       3173
## TGFBR3             131        821        858        469        817       1117
## VCAM1                0          4          4          0          1          3
## PTPN22              49        421        386        293        304        328
## CD160               28        179        159         48         76         83
## FCGR1A             122       2057        487        712       1599        980
## MCL1              5266      29112      32144      20046      25174      20895
## CTSK                 7         73         68         58         46         50
## RORC                12        190         10         28         73         50
## S100A9           25603      67773      96288      77156      96692      83363
## S100A12            793       2194       3453       1727       2550       1775
## S100A8           13625      25815      35110      29348      38916      31437
## IL6R               677       3127       4068       2050       4336       2442
## RIT1               232       1393       1602       1317       1030       1151
## BGLAP                3          6          7          5          8          6
## IFI16              328       1733       2107        857       2891       2082
## AIM2                22        133        115         29        153        148
## CRP                  0          0          0          0          0          0
## FCGR2A            1927       9362      11018       8141      12218       9240
## HSPA6              550       1020       1670       1010       1720       1119
## FCGR3A            1688      12990      15635       8824      16739       7326
## SELL              5395      30026      33539      21601      36535      24126
## GLUL              2732      15393      18196      13888      13377      16038
## PTGS2             1877      13311      10002       7709      15900      11698
## CRB1                 0          1          4          0          2          0
## KDM5B               73        502        583        384        438        409
## IL10                 1          6          6          6          3          3
## YOD1                38        455       1798        226        269        226
## HHAT                 7         37         47         20         34         46
## TRAF5               92        427        453        174        472        370
## NLRP3               78       1267       1124        660        903       1158
## LINC01250            0          0          1          0          0          0
## RPS7              2349      10215       6528       5646       9079       9139
## RSAD2               64        528       1101        678        999       2700
## FOSL2              490       4825       6043       4445       4220       4567
## REL                115       1677       1601        681       1155       1278
## TGFA               102        451        646        596        443        427
## DYSF               807       3348       4321       3007       5666       3346
## HK2                143       1465       1096       1882        956        932
## CD8A               340       1481       1238        837       1663       1576
## CD8B               138        634        401        435        945        768
## EIF5B              242        637        491        317        464        451
## IL1R1               39        298        223        163        209        185
## RGPD6               19        114        167         60         88         72
## IL1A                 1          1          2          2          0          0
## IL1B               174        925        804        742       1238        976
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             1083       1589       2369       2435       3895       3969
## NMI                273       1170       1111        795       1406       1156
## TNFAIP6             29        271        251        174        332        453
## IFIH1               54        458        453        259        637        515
## SCN1A                0          0          0          0          0          0
## ABCB11               0          0          2          0          3          2
## RBM45                9         48         73         25         47         58
## FRZB                 0          0          0          0          0          0
## TFPI                10          4         12          3          2          1
## STAT1              504       6371       4941       2001       6467       3901
## NABP1              186        790       1641        422        691        503
## SF3B1              553       5960       6630       3374       4771       4068
## CASP10              58        488        522        181        376        265
## CD28                79       1479       1016        515        812        794
## CTLA4               25        103         86         48         76         83
## ICOS                30        288        242        140        139        216
## NDUFS1              85        634        640        278        444        413
## CXCR2             2683      10228      13276       9126      18726      13991
## IRS1                19        162         50         82        109         96
## CCL20                0          2          1          1          4          2
## ATG16L1             61        348        348        266        328        285
## GPR35               28        112        131        225        121         99
## PDCD1                9         29         27         23         40         54
## PPARG                0          8          1          4          2          3
## RPL15             2957      14909      11791       8979      15287      14268
## EOMES               25        135        209         47        132        135
## CX3CR1             117        872        918        260        912        600
## ACKR2                1          1          1          4          1          0
## CCR2                36        761        878        180        544        302
## CCRL2                7         68         56         35         49         50
## TLR9                21         74         58         54         59         44
## ARHGEF3            206       1702       1259        717       1336       1102
## ADAMTS9              0          0          0          0          0          0
## TMEM45A              1          0          1          1          1          1
## CD80                 2         15         13         10          1          6
## CD86                70       1235        865        407        843        709
## MIX23                3         32         28          8         16         19
## PLS1                 4         36         22         11         14         24
## PTX3                12         90         52         57         72         51
## GOLIM4               3        136        102        104         69         69
## MYNN                42        424        442        238        316        320
## TNFSF10            258       2249       2288       1063       3516       2044
## ADIPOQ               0          1          0          0          0          0
## SPON2              243        277        726        200        343        630
## S100P              732       1456       3052       1491       1594       1165
## WDR1              1264       4562       5095       3922       4801       4511
## CD38                33        320        278         71        288        208
## PPARGC1A             0         10          6          0          2          1
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          1          0          0          0
## CXCL8             8302      45990      45998      52752      42605      73489
## CXCL2               11          8         12         29         18         45
## AREG                10         66         75        141         26        158
## CXCL10               0         33         18          1         58         12
## CXCL13               0          5          1          0          0          0
## SPP1                 4         39         47         40         11         84
## HERC6               36        220        263        151        249        281
## NFKB1              109       1048       1084        667        838        867
## SEC24B              91        597        604        362        517        378
## EGF                 35         53         46         32         16          9
## IL2                  0          0          0          0          0          0
## IL21                 0          0          0          0          0          0
## IL21-AS1             0          0          0          0          1          1
## SLC7A11              2         12         22         25         10          8
## IL15                20         79         84         24         73         59
## EDNRA                0          0          0          0          0          0
## TLR2               652       3341       4281       1803       3490       2740
## FGB                  0          0          0          0          0          0
## DDX60               47        497        892        296        620        696
## SPCS3              316       2785       2320       1049       1477       1602
## TLR3                 2         17         11          6         10          7
## OSMR                 3         60         83         25         42         38
## GZMK               164        718       1073        262        697       1007
## GZMA               270       1094       1157        595       1030       1299
## ANKRD55             17         61        100         77        136         36
## CENPK                1         47        105         25        105         36
## CAST               421       2959       2452       1247       3252       2221
## ERAP1              211       1436       1500        838       1196       1087
## ERAP2              353        315       1452       1060       2086       2785
## TNFAIP8            254       1905       1577        886       1221       1253
## CSF2                 0          2          0          1          0          0
## IL5                  0          2          1          0          0          0
## IL13                 0          2          0          0          0          0
## IL4                  2          4          7          0          7          1
## CD14               957       6450       7644       5646       8512       8943
## CSNK1A1            394       1535       1471        999       1403       1305
## PPARGC1B            14        256        152         73        171        111
## TNIP1              961       2733       4019       3292       4609       3852
## ATOX1              104        193        133        113        187        149
## FAXDC2             170        182        259        117        151        101
## IL12B                0          0          0          1          0          0
## MIR146A              0          0          1          0          0          0
## PDLIM7             560        711       1328       1315       1397       1339
## SERPINB1          1071       3285       3617       2974       4377       3517
## SSR1               245       2936       2291       1318       1900       1783
## CD83               144        932        769        436        949        983
## SOX4                28        184        201         66        141         93
## CMAHP               28        113        149        105        117         95
## HLA-A            12554      37983      45656      38465      36022      45446
## HLA-C            17374      38147      74638      60544      98151      62314
## HLA-B            29617      76749      91139      90256     117542     102496
## MICA                27        173        142         87        212        155
## LTA                 23         55         42         50        101         71
## TNF                 17        271        114         84        283        173
## HLA-DRB1           636       6440       3149       1736       4351       4251
## HLA-DQB1           191       1654        851        152        220        566
## PPARD               84        280        315        215        327        302
## CCND3             1722       3606       3423       4673       4561       4260
## VEGFA               25        218        201        377        234        199
## RUNX2              110       1031        554        567        475        590
## IL17A                0          5          1          1          0          0
## IL17F                0          2          0          0          0          0
## PRDM1              157        686        557        425        493        539
## ATG5                77        459        413        335        352        398
## TRAF3IP2            40        174        160        174        205        199
## NCOA7               54        603        373        216        391        411
## SGK1               296       4020       2881       4203       2668       3636
## IFNGR1             404       2088       2817       1665       1769       1716
## TNFAIP3            790       7927       6403       4604       6695       9336
## SOD2              6709      33968      49812      23071      44756      25461
## LPAL2                9         20         27          4         14         19
## PLG                  0          0          1          1          0          0
## CCR6                20        277         95         44         96         96
## RAC1               563       2385       2519       1748       2401       2110
## ZNF316             234        653        891        684        907        851
## AHR                 65       1877       1352        714       1154        735
## IL6                  3          6          9         12          7          8
## TOMM7              689       2498       2017       1836       2297       1853
## CYCS               136       1006        702        465        684        652
## AQP1                 2          4         10          2          5          2
## NT5C3A             296        664        721        520        763        614
## EGFR                 0          0          0          0          0          0
## CD36               174       2859       2840       1210       2263       1757
## SAMD9              175       1964       2306        852       2273       1871
## SERPINE1            13          7         11          8          4          7
## CUX1               333       1705       2051       1097       1880       1363
## PSMC2               55        420        311        203        268        273
## NAMPT             5347      41974      54764      34930      37058      36594
## HYAL4                0          0          0          0          0          0
## LEP                  1          1          2          2          1          2
## CALD1               32         11         21          8         10          7
## BRAF               114        763        960        653        751        727
## EZH2                10         94         51         44         59         64
## DNAJB6             426       1399       1369       1146       1143       1132
## CSMD1                0          0          6          0          9          0
## CTSB               649       6076       5891       3206       4642       3996
## EGR3               124        335        383        499        565        605
## TNFRSF10A           19        236        213        113        213        166
## BNIP3L             322       1955       5038       1105       1696       1436
## DUSP4               14        102         45         79         62         74
## NRG1                 6         32        125         91         96         97
## RPL7              3129      14647       8689       7050      11438      10131
## IL7                  5         24         23          2         10         11
## GEM                  0          1          3          5          0          3
## MYC                133        516        541        384        544        314
## GPT                  3          2          4          1          6          3
## JAK2               104       1442       1464        916       1292        908
## CD274               17        345        175        138        274        140
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              4          2          4          1          4          1
## TTC39B              57        333        346         57        227        102
## IFNA1                0          0          0          0          0          0
## TEK                  6         12         61          7          8         22
## TRBV20OR9-2          0          1          0          0          0          0
## TOMM5               68        254        176        139        202        181
## ANXA1              709      11744       6290       8417       5383       5769
## ERP44              229       1465       1286        879       1542       1106
## ZNF483               6         45        137         33         44         38
## TNFSF15              0          2          9          1          6          2
## TLR4               597       5784       6107       2575       7407       4968
## PTGS1              799        887        891        838        545        416
## HSPA5             1028       8341       4656       4887       6317       6764
## FNBP1              603       3373       2877       2135       3308       2833
## CARD9               39        167        176         79        236         84
## TRAF2               49        117        145         86        116        144
## CLIC3               76         62        131         46         98        105
## IL2RA               40        150         90        228         86        140
## GATA3              144        300        274        178        301        297
## VIM               2936      17449      15274      11756      12787      12691
## CREM                44        207        189        141        144        277
## DKK1                 0          0          1          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              184       1024       1196        703        782        764
## PRF1               661       1868       2360       1051       1831       2066
## ZMIZ1              267       2801       2944       2530       2925       2353
## IFIT3              738       5517       4178       4433       9678      12550
## TALDO1            3044       5602       8214       6568       8108       6335
## IGF2                 0          0          2          0          0          0
## INS-IGF2             0          0          2          0          0          0
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1              235       1246       1203        958       1299       1326
## TRIM22             379       2785       3159       1510       3100       2824
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          0          1          1          0
## SLC1A2               0          3          4          2          1          2
## FOSL1               22         84         40        146         45        109
## CCND1                2          9         10          2          3          4
## JRKL                25         99         72         34         76         60
## MMP7                 0          0          0          0          0          0
## MMP1                 7          6          2          0          0          0
## MMP3                 0          0          0          0          0          0
## CASP1              470       3196       2428       1437       3295       2167
## DLAT                32        175        143         73        185        137
## IL18                14         79         81         54         72         61
## CD3E               825       3327       2451       2183       3762       3323
## MCAM                63        312        248        214        290        244
## WNK1               478       4219       4120       2469       4790       3996
## TNFRSF1A           947       2370       2930       1671       4236       2264
## GAPDH             3187      17564      16166      13221      17814      15696
## CD4                353       5120       3805       2356       4290       3295
## SLC2A3            1692       7164      13068       8350       7380       9157
## CLEC4D              97        248        274        117        498        186
## KLRB1              169       1595        678        372        736        921
## CD69               701       4203       3137       4226       2730       3613
## CLEC2B             597       1813       1512       1168       1896       1776
## OLR1                 5         13          9         17          8         20
## ABCD2               15        357        495        109        232        195
## LRRK2              682       7568      12560       3500       8923       5278
## VDR                104        363        383        376        342        215
## TMBIM6            2253      11529      12373       8176      12355      10450
## PFDN5             1086       3954       2792       2386       3318       3074
## SP7                  0          0          1          0          1          0
## MUCL1                0          0          0          0          0          0
## CD63               983       2571       2483       3550       2229       2709
## SUOX               294        769        855        623        913        745
## RPS26              279       6217       3094       2808        712       4048
## RPL41             2559       6831       6059       5718       8263       8779
## IL23A                7         73         49         35         53         59
## DDIT3              314        708        688        607        509        437
## IFNG                14         58         53         39         93         94
## IL22                 0          1          1          1          1          1
## LYZ               6529      95893      64568      58632      88140      28068
## CAPS2                1          9         16          4          6         13
## SYT1                 2          6          9          0          3          2
## BTG1              3636      10240       9857       8534       9580      11095
## HCAR3              475       1727       2085       1170       4265       2343
## GJB2                 0          1          3          0          1          0
## GJB6                 9         21         51         14         17         11
## TNFSF11              0          2          8          0          3          1
## TPT1             11528      67676      41529      37672      58292      51586
## LMO7                11         99         91         42         98         78
## TNFSF13B           524       2042       2379       1528       2640       2070
## LAMP1              703       2418       3024       2033       3080       2405
## PSME2              258       2106        912        803       1961       1232
## GZMB               307        635       1044        678        931       1167
## RPL36AL            770       2654       1909       1797       2549       2268
## PYGL               792       3117       4797       4279       4558       3269
## HIF1A              220       4138       3924       5103       2065       2906
## FOS              13062      70672      55320      71693     116448      60188
## JDP2               144        571        702        672        642        600
## NOXRED1              3          5         15          4          7          9
## SERPINA1          4405      20313      17113      17232      25482      17226
## CDC42BPB            35        248        219        130        318        218
## PLA2G4D              0          0          0          0          0          0
## TRIM69              10         15         12         10         12         21
## SLC51B               0          0          0          0          0          0
## SMAD3              141        820        668        625        624        862
## CYP1A1               0          1          1          0          0          0
## AKAP13             679       7171       6271       3586       5789       4669
## MEFV               450       2008       2552       1402       2535       1979
## SOCS1               46         92        141        167        127        139
## ATXN2L             323       1565       1631       1287       2546       1763
## CD19                57         75         81         41        138        197
## ITGAL             1438       5571       5250       4091       5954       5472
## ITGAM              948       4394       5015       6564       5941       4392
## ITGAX             1200       4423       4591       4954       5275       4194
## DNAJA2             127        718        650        401        536        574
## SIAH1               34        157        299        137        113        114
## ADCY7              235       2412       2527       1242       3242       2180
## NOD2               103        632        531        901        641        770
## CMTM2              726       1177       1505        951       1524       1670
## SF3B3              174       1087       1001        502       1017        917
## PSMD7              199        813        800        572        643        611
## WWOX                 8         55         52         25         52         48
## MAF                 99        702        452        387        502        572
## SLC7A5              39        209        311        263        266        211
## CXCL16             421       1489       2084       1875       2045       1567
## XAF1               166       1069        784        751       1567       1566
## CD68               336       4438       3563       1848       3643       2991
## PER1               521       1091       1074       1152        637        998
## NOS2                 1          0          2          0          2          5
## TRAF4               28        114         84        101        110        116
## CCL2                 0         22         16         32         39         18
## CCL5              2350       2459       4442       2880       4782       5910
## CCL3               127        339        307        129        580        281
## CCR7               114        715        956        432        982        627
## STAT3              900       3660       4254       2506       4456       3568
## SOST                 0          0          1          0          0          0
## ITGA2B             720        458        433        735        190        177
## EFCAB13              5         39         71         12         29         31
## NPEPPS             142        713        903        448        794        586
## TBX21              162        312        387        195        350        383
## COL1A1               0          2          1          1          0          2
## MRPS23              25        145        133         85        102        116
## MIR21                1          3          9          2          3          4
## RPS6KB1             55        453        439        185        372        333
## ACE                 11         96         34         27         57         99
## ERN1               263       1438       1194        631       1192       1273
## PRTN3               10          1         14         32          6         22
## PLIN5               99         35         84         71         74         98
## RETN                35         42         45         74         94         51
## CCL25                0          0          1          1          2          0
## ICAM1              269       2202       2266       1723       2209       1537
## TYK2               558       1158       1696        992       1977       1172
## SMARCA4            153        655        702        454        822        674
## ACP5                78        212        297        243        239        376
## JUNB              6875      14364      30448      31767      40361      36681
## CYP4F22              5         32         51          9         13         15
## JAK3              1130       1481       1981       1359       2262       1545
## JUND              8145       5683      10923      13363      15719      15514
## CEBPA              184        525        906        395        781        408
## CEBPG               39        397        356        161        240        267
## ACP7                 0          0          0          0          0          0
## ZFP36             4950      19016      24419      33030      34949      38595
## TGFB1             1425       3049       4595       4621       5528       4884
## RPS19             4515      10811       9687       7693      11605      12425
## PSG2                 0          0          0          0          0          0
## FUT2                 2          2          3          1          6          4
## NKG7              1567       2725       4145       2787       4136       5925
## ZNF415               1          3          7          1         11         11
## LILRB2             622       3233       4167       3405       4734       3536
## LILRA5             854       1031       2834       1881       3081       1385
## KIR3DL1             19         36         62         13         78         74
## KIR3DL2             17         46         92         25         66         53
## SMOX               212        121        169        106         64         62
## BMP2                 2          5         10          4          9          4
## GINS1                2          8          5          3         12          5
## PLCG1              168       1129        828        458       1038        764
## YWHAB             1470       6209       5230       3628       5740       5075
## PI3                507        300        603       1786       1332        897
## MMP9               718        715       1546       1188       2650       1095
## CD40                47        199        128         75        156        177
## PFDN4               25         62         66         34         52         49
## BMP7                 0          0          1          0          0          0
## RPS21             1675       4539       3689       3372       5219       5113
## MX1                359        774       1264       1476       2647       3512
## PFKL               243       1123       1106        679       1273       1106
## IL17RA            1070       3433       4532       3372       6313       4028
## UBE2L3             235        880        794        696        973        779
## TPST2              374        914       1242       1037       1242       1289
## XBP1               155       1161       1034        692        771        958
## UQCR10             163        557        467        403        517        409
## SEC14L2              2         45         45         17         65         24
## APOL6              282       3388       2886        809       2733       1731
## APOL1              129        960        629        352       1188        456
## TYMP              1620       2361       2893       2237       6635       3402
## BEND2               64         81         74         29         28          8
## PHEX                 1         20         14          9         15         17
## TIMP1              660       1296       1295       1090       1105       1918
## FOXP3               39         89         48         47         89        110
## MSN               3732      23134      22106      17165      24087      22416
## PGK1               836       8643       7714       6487       7031       6243
## LAMP2              808       5675       7219       4188       5567       4880
## CD40LG              24        282        127         76        194        136
## IRAK1              225       1491       1436       1257       1664       1486
## COX2            136097      54310      47314      48572      61407      42088
##             GSM3308455 GSM3308456 GSM3308457 GSM3308458 GSM3308459 GSM3308460
## TNFRSF9            171         56         21         76        125         83
## ENO1              6844       4057       2065       5220       5229       6741
## PIK3CD            7189       4870       3539       5226       5532       6723
## PGD               6152       3574       2569       4014       6170       4097
## MTHFR              675        405        130        423        301        683
## TNFRSF1B         16775       9584       5269      13269      11950      13896
## PINK1              870        573        426        741        840        673
## IFNLR1              79         33         20         70         56         85
## RUNX3             4051       2816        660       6894       2144       4168
## SH3BGRL3         13172       6335       9410      11034       9351       9371
## CD52              4505       2712       1559       6010       2661       3654
## IFI6               932        858       4948       1351       1497       1124
## ZC3H12A            754        135         71        672        415        440
## UTP11               66         69         37         78         54         93
## JUN              20323       1320        348      20068       5658       5071
## KANK4                1          0          0          0          0          1
## EFCAB7              28         22         10         21         23         28
## IL23R                0          4          0          5          4          2
## ADGRL2               0          0          0          0          0          0
## GBP3                89        146         65        140        197        206
## GBP1               671        647        412       1053        900       1079
## GBP5              2219       1772        572       4360       4376       3372
## TGFBR3            1108        579         72       1217        295        943
## VCAM1                6          1          0          4          0          0
## PTPN22             282        333         45        332        251        469
## CD160               99         95         18        131         77        109
## FCGR1A             741        225        388        829       1062        682
## MCL1             28602      15873       6216      22083      29429      21974
## CTSK                71         35          4         60         28         66
## RORC                32         31         10         53         38         39
## S100A9          143859      50814      50839      64526     148159      55804
## S100A12           6059       1483       1829       1460       3384       1425
## S100A8           60418      18834      21795      22682      55687      20879
## IL6R              4670       3262       1091       2818       4077       3719
## RIT1              1613        806        273       1425       1538       1098
## BGLAP                8          3          6          5          5          6
## IFI16             1794       2226        904       1390       3014       2472
## AIM2                88         69         42        103        259        107
## CRP                  0          0          0          0          0          0
## FCGR2A           11451       7834       2046       8011      12979       9756
## HSPA6             1458        926       1318       1250       1872       1126
## FCGR3A            9118      13429       2364      15899      22838      16908
## SELL             35112      18968       8161      32776      45843      20504
## GLUL             16972       7911       4082      12457      11283      10618
## PTGS2            16565       2448       1193       4810       7389       7621
## CRB1                 2          1          0          2          0          2
## KDM5B              487        316         92        385        482        409
## IL10                 2          2          0          5          9          5
## YOD1               227        171         39        284        326        316
## HHAT                37         27          3         50         27         53
## TRAF5              265        248        115        344        226        484
## NLRP3             1525        543         66        720        664        891
## LINC01250            0          1          0          0          0          1
## RPS7              7204       4845       2591      12050       6082       8840
## RSAD2              275        455       2043        593        671        527
## FOSL2             4395       1721        482       4923       2902       3467
## REL               1193        923         93       1267        928       1287
## TGFA               353        340         97        396        685        364
## DYSF              6128       2730        881       2455       6672       3676
## HK2               1559        585        182        765       1072       1004
## CD8A              3108        895        208        810       1018       1682
## CD8B              1310        394        137        333        578        595
## EIF5B              354        366        249        476        297        553
## IL1R1              243        152         35        236        294        221
## RGPD6               48         73         12         73         49         81
## IL1A                 1          0          0          0          0          0
## IL1B               846        154        261        197        217        471
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             3220        892       2802       2073       2178       2093
## NMI               1300        820        628       1171       1779       1148
## TNFAIP6            428        435        110        167        659        463
## IFIH1              362        285        170        338        390        449
## SCN1A                0          0          0          0          0          0
## ABCB11               2          2          0          0          0          2
## RBM45               38         49         18         43         29         70
## FRZB                 0          0          0          0          0          0
## TFPI                 1          3         22          3          3          0
## STAT1             3628       2666       1238       3727       3536       4601
## NABP1              580        353        187        309        657        610
## SF3B1             4433       2855        412       3796       3689       5046
## CASP10             260        302         97        319        256        373
## CD28               345        262         92        853        243        650
## CTLA4               78         22         14        110         40         72
## ICOS               112         74         43        210         59        144
## NDUFS1             466        438        102        408        421        528
## CXCR2            11372      13483       3395       9838      19712      11693
## IRS1                56         38         53        107         80        117
## CCL20                4          0          3          7          6          2
## ATG16L1            279        170         78        323        193        368
## GPR35              130         26         23        125         88        115
## PDCD1               44         66          7         39         25         28
## PPARG                9          4          1          6          5          2
## RPL15            12575       8820       3858      19454      10129      14545
## EOMES              137        144         55        141         72        150
## CX3CR1            1343       1397        238        381        424       2183
## ACKR2                2          2          0          0          0          3
## CCR2               625        845         66        345        618        654
## CCRL2               30         33         15         30         34         33
## TLR9                54         38         48         63         82         53
## ARHGEF3           1230        721        206        996        635       1170
## ADAMTS9              0          0          0          0          0          0
## TMEM45A              4          1         11          2          7          1
## CD80                 4          3          1          5          3          4
## CD86               905        828         85        919        576       1077
## MIX23               17         18          9         15         11         20
## PLS1                 8         11          1         21          7         21
## PTX3               121          9          7         63         36        105
## GOLIM4              66         84          7         76         62        102
## MYNN               273        200         54        336        292        339
## TNFSF10           2178       2517        667       1596       2670       2458
## ADIPOQ               0          0          0          0          0          0
## SPON2              383        469        339       1370        276        677
## S100P             4830       2056        179       3567       4437       1373
## WDR1              6117       3864       2345       4802       4984       5777
## CD38               149        252         45        370        189        308
## PPARGC1A             6          3          0          1         10          4
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          0          0          1          0
## CXCL8            91307       4435       1002      58664      28348      31644
## CXCL2               50          5          5         10         19         10
## AREG                68         43          2        232        216         68
## CXCL10              12         10          2         15         12         34
## CXCL13               0          0          0          2          0          0
## SPP1                48         16          1         88         11        116
## HERC6              143        170        194        166        150        205
## NFKB1              699        646        118        794        612        861
## SEC24B             412        385         82        438        375        450
## EGF                 51         29        176         27         36         23
## IL2                  1          1          1          1          0          1
## IL21                 0          1          0          1          2          3
## IL21-AS1             1          1          0          1          1          2
## SLC7A11             18          4          3         17          7         15
## IL15                94         73         17         56         52         67
## EDNRA                0          0          0          0          0          0
## TLR2              4634       3293        712       2577       8913       3056
## FGB                  0          0          0          0          0          0
## DDX60              295        375        262        323        342        433
## SPCS3             1629       1472        422       1471       1640       2039
## TLR3                 9         14          0         12          3         15
## OSMR                34         20          0         27         22         45
## GZMK               702        356         48        978        440        722
## GZMA              1445        883        253       1477        550       1138
## ANKRD55             47         66         29        115         96         98
## CENPK               77         45          4         73         71         24
## CAST              3602       2820        643       1784       2304       2783
## ERAP1             2069       1117        192       1819       1571       1522
## ERAP2              160        121        168       1842        163       2118
## TNFAIP8            935        848        332       1281       1013       1337
## CSF2                 0          0          0          1          0          1
## IL5                  0          0          0          1          0          0
## IL13                 0          1          0          0          1          1
## IL4                  2          1          0          2          0         12
## CD14             10796       3123       1403       5649       6901       8134
## CSNK1A1           1425       1239        675       1269       1324       1532
## PPARGC1B           139         93         13        133        117        260
## TNIP1             5357       2717       1762       3824       5265       4097
## ATOX1              173        146        150        159        142        195
## FAXDC2             151        134        504        194         96        175
## IL12B                1          0          0          0          1          2
## MIR146A              0          0          0          1          0          0
## PDLIM7            2135        817        944       1339       1582       1110
## SERPINB1          4266       2901       2020       2988       4276       3049
## SSR1              2157       1553        375       1978       2038       2381
## CD83               969         54         36        804        210       1069
## SOX4               206        166         88        244        158        284
## CMAHP               64         28         40         78         49        117
## HLA-A            40930      33811      23078      61099      44929      38608
## HLA-C           100979      56611      20105     102535      62214      59345
## HLA-B            89597      69694      28025     115037     103222      89831
## MICA               116         97         82        105        108        192
## LTA                 44         39         26         55         22         76
## TNF                167         21         34        189         65        258
## HLA-DRB1          3816       4763        587       6509       1979       7286
## HLA-DQB1           302       1454        208       1675        259       1666
## PPARD              241        208         86        392        226        320
## CCND3             4461       3295       3641       6087       7379       3800
## VEGFA              231        104         18        285        151        192
## RUNX2              562        355         92        784        590        506
## IL17A                0          0          0          0          0          0
## IL17F                0          0          0          0          0          0
## PRDM1              698        785        143       1040        939        586
## ATG5               342        240         63        428        332        388
## TRAF3IP2           157        107         75        250        179        204
## NCOA7              303        287        103        346        299        384
## SGK1              4036       2076        270       1452       2008       2661
## IFNGR1            2096       2881        406       1771       4214       2262
## TNFAIP3           6952       2588        166       8263       9672       3603
## SOD2             46517      22619       6833      30687      36424      36188
## LPAL2               14          4          2         13         13         19
## PLG                  0          0          0          0          0          1
## CCR6                44         74         68        116         33        110
## RAC1              2782       1879       2120       2560       2443       2639
## ZNF316             799        402        289        851        578        665
## AHR               1238        718         61        855        960       1240
## IL6                  4          2          1          4          2          5
## TOMM7             1946       1267        877       3552       1742       2506
## CYCS               668        368        122        679        421        660
## AQP1                 5          1         10          3          5          5
## NT5C3A             627        414        917        674        741        598
## EGFR                 0          0          0          0          0          0
## CD36              4296       2002        250       1517       2265       2572
## SAMD9             1494       1198        432       1117       1916       1906
## SERPINE1             7         15         14         12          6         14
## CUX1              2110       1349        503       1713       1701       2216
## PSMC2              329        257         77        341        206        347
## NAMPT            50943      23177       5259      35418      62489      32898
## HYAL4                0          0          0          0          0          1
## LEP                  2          2          4          7          3          6
## CALD1               23         13         67         24          1         19
## BRAF               795        472        125        679        576        861
## EZH2                39         43          8         66         35         74
## DNAJB6            1356        878        693       1357       1283       1354
## CSMD1                0          3          0          4          0         17
## CTSB              5421       4227       1221       6010       5011       5388
## EGR3               645         53        116        255        232        359
## TNFRSF10A          111         70         21        153        108        176
## BNIP3L            2149       1601        558       1672       1957       2030
## DUSP4               82         10          6        185         20         49
## NRG1               301        127         17        155        125        163
## RPL7              8357       6449       4489      14071       7488      11016
## IL7                 13         11          6          7          9         18
## GEM                  0          1          0          2          0          0
## MYC                307        651        212        592        574        622
## GPT                  1          4          0          2          1          4
## JAK2              1310        821        158        759       1419        942
## CD274               94         63         34        181        220        107
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              2          1          5          2          2          1
## TTC39B             103        132         61        152         74        161
## IFNA1                0          0          0          0          0          0
## TEK                  1          3          9          4         37         56
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              193        141         72        239        164        248
## ANXA1             7419       5235        843       8028       4641       7586
## ERP44             1409        819        289       1247       1243       1349
## ZNF483              22         29          8         28         11         41
## TNFSF15              5          5          0          0          6         14
## TLR4              5614       5603        783       2237       9913       4835
## PTGS1              939        573       3239        833        493        762
## HSPA5             5573       2254       1314       6184       4272       4604
## FNBP1             3044       2688        623       3384       3172       3297
## CARD9              202        122         61         90        117        232
## TRAF2               93         84         61        122         73        147
## CLIC3              117        118        109        249         59        101
## IL2RA               72         77         22        135         68        156
## GATA3              239        259        163        423        115        331
## VIM              23313      12039       3940      13546      12311      14938
## CREM               131         82         54        264        119        132
## DKK1                 0          0          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              843        570        259        812        679        761
## PRF1              1981       2379        792       2768       1045       2683
## ZMIZ1             3077       1618        246       2816       1962       2313
## IFIT3             2746       2291       6447       4647       5511       4067
## TALDO1            9697       5238       4282       6621       8968       6688
## IGF2                 0          0          0          0          0          1
## INS-IGF2             0          0          0          0          0          1
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1414        968        297       1395       1041       1524
## TRIM22            1681       1966       1748       1834       3465       2351
## PTH                  0          0          0          0          0          0
## SAA1                 1          0          0          1          0          0
## SLC1A2               0          0          0          1          2          2
## FOSL1               62          2         14         26         38         33
## CCND1                6          2          7          8          5         16
## JRKL                57         85         14         66         47        107
## MMP7                 0          0          0          0          0          1
## MMP1                 1          0          8          3          0          5
## MMP3                 0          0          0          0          0          0
## CASP1             2367       1827        738       2277       3074       2575
## DLAT               151        129         18        176        112        185
## IL18                71         62         17        100        103        104
## CD3E              2819       1766        824       3676       1899       3300
## MCAM               304        141         59        260        215        295
## WNK1              4625       3194        410       3440       3652       4197
## TNFRSF1A          3632       2257       1517       2342       3439       2770
## GAPDH            22309      12305       6967      19306      18374      16707
## CD4               4230       3274        269       3684       2317       4749
## SLC2A3           11014       3382       1782       9105       8997       7950
## CLEC4D             435        271        131        301        553        236
## KLRB1              550        698        389       1631        804        866
## CD69              3042        476         88       2347       1463       1541
## CLEC2B            1639        879        743       1632       1636       1478
## OLR1                19          3          3          2          7          3
## ABCD2              148         98         24        126         87        224
## LRRK2             8698       5774        619       5202      13389       8035
## VDR                390        335        168        223        411        273
## TMBIM6           13794       8482       2915      10519      12183      12958
## PFDN5             3136       2079       1764       4056       2415       3581
## SP7                  0          0          0          1          0          0
## MUCL1                0          1          0          1          0          0
## CD63              3013       1399       1483       2935       3086       2670
## SUOX               969        730        400        873       1051       1030
## RPS26             3009       2119        452        980       2354       3962
## RPL41             6491       4313       3334      10846       5686       7787
## IL23A               26         25         13         67         14         34
## DDIT3              654        136        335        544        455        462
## IFNG               212          8          2         65         15         49
## IL22                 0          0          0          0          0          0
## LYZ             130738      73441       4865      53788      93617     107609
## CAPS2                3          2          0          5          0          7
## SYT1                 1          9          0          2          8          2
## BTG1             10617       6644       3200      15515      11476       9724
## HCAR3             2701        587        297       1016       1825       1954
## GJB2                 2          0          0          1          1          6
## GJB6                24          5          2         37         14         17
## TNFSF11              1          5          0          9          4          5
## TPT1             46600      32893      13786      70299      42053      55402
## LMO7                36         55         12         58         49        121
## TNFSF13B          1835       1589       1037       1533       1911       1457
## LAMP1             2936       2075        921       2711       2577       3059
## PSME2             1100        742        546       1581        874       1342
## GZMB              1063        889        366       2181        421       1456
## RPL36AL           1920       1216        988       2688       1928       2454
## PYGL              6179       3074        818       2730       6452       3471
## HIF1A             2410       1339        220       3644       2182       2038
## FOS              95888      25470       8105      81337      56248      35824
## JDP2               727        623        256        781       1995        582
## NOXRED1             14          3          1          6         13         11
## SERPINA1         24380      14432       6031      21178      29357      18263
## CDC42BPB           261        261         51        269        197        342
## PLA2G4D              0          0          0          0          0          0
## TRIM69              10          9          5          8          7         16
## SLC51B               0          0          0          0          0          0
## SMAD3              608        405        127        760        436        723
## CYP1A1               0          3          0          1          3          2
## AKAP13            4685       3605        698       5557       5751       5524
## MEFV              2669       2050        524       1807       2690       2051
## SOCS1               62         88         72        143        134         78
## ATXN2L            1755       1370        226       2205       1175       2023
## CD19                91         67        101        143        102        152
## ITGAL             7207       4609       1345       5246       4335       6785
## ITGAM             5657       3947       1250       4634       6765       4786
## ITGAX             5837       2110        973       3472       4553       5018
## DNAJA2             570        521        196        576        571        587
## SIAH1              107        100         61        127         84        131
## ADCY7             2805       2192        221       2582       2682       3312
## NOD2               573        525         85        369        716        854
## CMTM2             2426       1375        784       1717       3055       1515
## SF3B3              795        614        210        767        593       1087
## PSMD7              689        441        222        742        546        736
## WWOX                51         33         12         72         37         71
## MAF                409        318        139        534        269        730
## SLC7A5             242        116         77        473        169        270
## CXCL16            2695       1444        287       2520       2554       2152
## XAF1               579        629        861        675        777       1130
## CD68              4295       3277        662       3756       3311       4436
## PER1               771       1199        209       1757       2710        867
## NOS2                 0          0          0          0          0          5
## TRAF4              103         30         26        189         43        127
## CCL2                10          2          4          3          6         34
## CCL5              7086       3003       4154       5103       2301       5364
## CCL3               414        124        185        309        151        175
## CCR7               275        663        368        864        528        829
## STAT3             4095       3399       1343       3514       4747       4148
## SOST                 0          0          2          0          0          0
## ITGA2B             695        313       4211        478        232        507
## EFCAB13             19         13          1         30         19         30
## NPEPPS             836        662        155        605        769        819
## TBX21              472        261        161        509        147        483
## COL1A1               0          0          0          1          1          1
## MRPS23             116        139         52        131         84        148
## MIR21                3          3          0          4          3          2
## RPS6KB1            297        260         78        336        295        407
## ACE                 44         29         11         66         24         63
## ERN1              1195       1166        164       1304       1369       1573
## PRTN3                2          5         55          3         24          3
## PLIN5              114         48        112         42        130         67
## RETN               154         20        113         51         46         12
## CCL25                0          0          2          1          1          0
## ICAM1             2216        525        216       1817       1109       1429
## TYK2              1661       1332        689       1085       1610       1585
## SMARCA4            640        538        226        764        484        777
## ACP5               204        321        122        221        253        243
## JUNB             37990       6947       6873      53240      26993      20662
## CYP4F22             58        108         13        128          9        190
## JAK3              1939        809       2470       1236       1292       1598
## JUND             15330       2439       5796      14165       6179       6224
## CEBPA             1153        425        251        828        586        878
## CEBPG              264        227         68        239        182        306
## ACP7                 1          0          0          3          0          0
## ZFP36            42723       5930       3802      32192      18942      14652
## TGFB1             6378       2836       3288       6006       4778       4219
## RPS19             8530       6537       7662      14764       6639      11260
## PSG2                 0          0          0          0          0          0
## FUT2                 2          1          8          2          0          3
## NKG7              6852       2477       1843       6202       2157       4537
## ZNF415               7          3          0          3          9          8
## LILRB2            4463       3291        560       4059       3902       4231
## LILRA5            2083       1808       1877       1674       2110       1530
## KIR3DL1             39        190         11        257         90         57
## KIR3DL2             25         24         10        192          7         27
## SMOX               114         62        704        139        104         61
## BMP2                 4          2          1          5          4          5
## GINS1                5          3          3          3          7         11
## PLCG1              543        547        188        768        471        971
## YWHAB             5638       3557       1687       4444       5084       5949
## PI3               1511        360        287        227       1136        343
## MMP9              3975       1320       1169       1820       3970       1322
## CD40               136        115         84        199        125        201
## PFDN4               44         34         23         53         32         55
## BMP7                 0          0          0          0          0          0
## RPS21             3578       2692       1913       7142       3424       4665
## MX1                883        981       2820        760        949       1712
## PFKL              1204        854        355       1231        773       1309
## IL17RA            5961       4926       1413       4540       7707       4768
## UBE2L3             980        705        515        908        848       1010
## TPST2             1823        819        814       1383       1019       1244
## XBP1               839        677        365       1284        652        817
## UQCR10             464        347        254        617        426        559
## SEC14L2             11         21          8         39         19         29
## APOL6             1119       1083        810       1719       1373       1655
## APOL1              541        461        297        673        554        652
## TYMP              4321       1627       3882       3045       3062       3786
## BEND2               68         43        333         84         12         54
## PHEX                15          5          2         25          5         14
## TIMP1             1750       1385       1211       1516       2170       1174
## FOXP3               57         45         35         81         44         69
## MSN              28636      17459       4505      21074      25441      23087
## PGK1              8436       4369       1012       6732       7015       7442
## LAMP2             6862       4517        786       5205       8214       5884
## CD40LG              76        131         38        187         73        183
## IRAK1             1696        801        279       1916       1314       1719
## COX2             53689      34513     224597      85345      37834      46152
##             GSM3308461 GSM3308462 GSM3308463 GSM3308464 GSM3308465 GSM3308466
## TNFRSF9            140        177         71        122        224        283
## ENO1              5089       6984       5744       6257       7165       6578
## PIK3CD            8324       7112       6609       7134       5200       8675
## PGD               5458       6080       4757       5740       4419       8786
## MTHFR              456        494        454        314        360        409
## TNFRSF1B         13075      16553      16909      14482      12367      15082
## PINK1              970        936        732        957        629       1066
## IFNLR1              45         98         47         59         77         49
## RUNX3             3460       2879       4128       3907       3621       2662
## SH3BGRL3          8650      10044      11673      12686      12570      13369
## CD52              2989       4093       3331       4484       5161       2625
## IFI6               510       5623       5129       3634       2373       1325
## ZC3H12A            491        311        508        557        530       1184
## UTP11               71        134         86         87         69         74
## JUN              10163       5429       1370      10743      18149       7780
## KANK4                0          0          0          1          0          0
## EFCAB7              31         40         25         24         16         14
## IL23R                0          0          1         11          5          1
## ADGRL2               0          0          0          0          0          0
## GBP3               239        195        172        137        265        303
## GBP1               677       1511       1441        882        854       1907
## GBP5              2172       3657       3029       2553       2550       4707
## TGFBR3             643        430       1403        841        865        573
## VCAM1                2          4          2          2          4          6
## PTPN22             331        524        447        380        303        277
## CD160              163         46        164        145        200         41
## FCGR1A             522        535        563        599        840       1719
## MCL1             27351      19651      20489      24814      21244      39068
## CTSK                69         29         52         32         40         55
## RORC                36         42         54         54         46          7
## S100A9          142511     116253     102066     163151     119400     217249
## S100A12           6976       3409       2818       5461       3283       9373
## S100A8           51105      38493      38190      62082      46546      85549
## IL6R              5292       5108       4758       5307       3512       5400
## RIT1              1509       1357       1312       1400       1198       1872
## BGLAP                5          4          9          7          5          7
## IFI16             2325       5326       5494       4036       2443       3805
## AIM2               197        164        155        170        190        324
## CRP                  0          0          0          0          0          0
## FCGR2A           15816      14311      16678      18568      12047      16618
## HSPA6             1882       2213       2920       2333       1430       2086
## FCGR3A           19242      21704      26233      25078      14703      23559
## SELL             46154      38917      41920      49800      33623      51861
## GLUL             15195      14101      15830      17034      11108      23426
## PTGS2            13720      11508       2975      17731      10594      29561
## CRB1                 2          1          1          0          0          1
## KDM5B              478        486        552        432        356        551
## IL10                 2          0          4          0          7          2
## YOD1               262        167        291        172        220        226
## HHAT                39         43         23         31         30         13
## TRAF5              359        310        373        240        316        171
## NLRP3              893        991        804        871        917       1343
## LINC01250            0          0          0          0          1          0
## RPS7              7439       7389       7128       7937       9624       5068
## RSAD2              137       4156       6957       2162       1698        649
## FOSL2             4388       3971       3032       3264       3485       7253
## REL               1133       1334       1381        844        839       1092
## TGFA               681        522        464        572        362        818
## DYSF              7081       4859       5268       6676       4740      10257
## HK2               1115       1486       1041        892        973       2163
## CD8A              1367       1103       1202       1797       2451        996
## CD8B               788        534        522        888       1121        243
## EIF5B              499        479        481        409        496        377
## IL1R1              331        223        232        219        196        252
## RGPD6               63         74         83         46         62         56
## IL1A                 0          0          1          0          1          9
## IL1B               604        760        550       1502        882       4056
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             3099       3043       4435       4639       4784       7994
## NMI               1444       1770       2488       1851       1213       2389
## TNFAIP6            287        828        792       1239        599       1343
## IFIH1              343        811        928        530        503        598
## SCN1A                0          0          0          0          0          0
## ABCB11               0          3          0          0          0          3
## RBM45               48         42         56         60         56         41
## FRZB                 1          0          0          0          0          0
## TFPI                 5          2         11          5          6          3
## STAT1             2977       6063       5807       4432       4415       6631
## NABP1              722        638        607        704        571       1114
## SF3B1             4802       4494       4796       4180       3647       4949
## CASP10             283        416        395        238        270        339
## CD28               621        521        615        475        607        349
## CTLA4               47         60         63         74         60         56
## ICOS               179        104        168        182        171        145
## NDUFS1             444        533        635        473        390        475
## CXCR2            20634      23466      29481      29974      13890      22692
## IRS1                55        132         68        106        144         32
## CCL20                1          0          1          1          5          5
## ATG16L1            283        258        298        208        242        208
## GPR35               71        148         83         75        119         65
## PDCD1               41         36         26         34         34         41
## PPARG                1          2          3          2          6          1
## RPL15            12035      12743      12111      12877      15168       8044
## EOMES               93         79        183        134        122        136
## CX3CR1             871       1840       2175       1014       1143       1945
## ACKR2                0          0          0          0          2          1
## CCR2               465       1785        847        550        434        536
## CCRL2               25         50         43         36         35         59
## TLR9                66        113         69         65         43         56
## ARHGEF3           1131        940       1478        869       1176       1000
## ADAMTS9              0          0          0          0          1          0
## TMEM45A              1          8          2          2          0          0
## CD80                 4         13          6          4          8          1
## CD86               601       1511        777        741        697        713
## MIX23               21         27         25         25         23         19
## PLS1                17          6         22         21         14          9
## PTX3                57         55         41         49         83        138
## GOLIM4              62        139         72         49         60         67
## MYNN               276        348        343        294        261        436
## TNFSF10           2985       5450       5035       4840       2499       4249
## ADIPOQ               0          0          0          0          0          0
## SPON2              366        479        843        322        482        596
## S100P             4714       2668       1468       2655       3876        918
## WDR1              5752       6360       6675       6188       5467       6309
## CD38               208        347        270        190        252        352
## PPARGC1A             4          4          1          3          2          3
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          1          0          0          0
## CXCL8            29532      30376      17855      42655      65930     108930
## CXCL2               10         18          8         27         22         63
## AREG                23         64          7         29         30        147
## CXCL10               9         22         31         22         34         37
## CXCL13               1          3          1          2          0          2
## SPP1                62         33         79         18         28         56
## HERC6              155        391        527        241        322        168
## NFKB1              935        897       1077        775        751       1057
## SEC24B             478        498        560        341        386        406
## EGF                  9         14        113         41         55          8
## IL2                  0          2          1          3          1          1
## IL21                 1          2          1          0          2          4
## IL21-AS1             3          1          2          3          5          3
## SLC7A11             15          9         20          9          9         16
## IL15                89        116         71         72         70         89
## EDNRA                0          1          0          0          0          0
## TLR2              4074       3214       3934       4324       3494       4797
## FGB                  0          0          0          0          0          0
## DDX60              213        988       1390        564        663        390
## SPCS3             1799       2380       1994       1742       1755       1959
## TLR3                10          5         23          5         12          8
## OSMR                42         30         53         35         21         30
## GZMK               628        183        668        682        819        609
## GZMA              1071        524       1764       1658       1634       1265
## ANKRD55            105         42         70         63         58         81
## CENPK               66         66        119         22         26         18
## CAST              2363       2880       3623       2171       2336       2968
## ERAP1             1272       2283       2036       1272       1403       1144
## ERAP2             1428        159       1788       2629        142       1322
## TNFAIP8           1336       1397       1717       1158       1175       1069
## CSF2                 0          0          0          0          0          0
## IL5                  0          2          0          1          0          0
## IL13                 0          0          0          0          0          0
## IL4                  1          3          3          4          4          4
## CD14              5164      12149       7434       9002       7667      11681
## CSNK1A1           1557       1885       1708       1523       1354       1762
## PPARGC1B           122        121         99         99        132        129
## TNIP1             4789       4850       5449       5916       4080       6197
## ATOX1              153        185        206        184        177        202
## FAXDC2             101        137        284        149        208         96
## IL12B                1          2          1          0          1          0
## MIR146A              0          1          0          0          1          0
## PDLIM7            1870       1491       1601       2154       1379       2026
## SERPINB1          4574       4671       4664       5455       5317       5693
## SSR1              1812       2886       2371       2194       2325       2418
## CD83               329        418        468        385        630       1316
## SOX4               139        160         82        144        181        134
## CMAHP               54        100        102         38         62         66
## HLA-A            43706      53402      52797      44242      42077      45235
## HLA-C            90906      63703     106014     119261      83981     109743
## HLA-B            95532     114541     119279     116613     127056     137452
## MICA               125        173        129        124        101        109
## LTA                 70         47         69         48         59         35
## TNF                149        144        221        308        315        387
## HLA-DRB1          1594       6786       3063       4529       7066       3605
## HLA-DQB1           178       1543        199       1102       1038        869
## PPARD              298        337        562        239        224        188
## CCND3             3873       4378       3973       4737       4659       5193
## VEGFA              133        216        109        143        226        169
## RUNX2              459        502        607        438        402        443
## IL17A                0          0          0          0          0          0
## IL17F                0          0          0          0          0          0
## PRDM1              505        535        829        630        511        579
## ATG5               291        431        408        323        346        360
## TRAF3IP2           230        234        223        191        210        117
## NCOA7              304        508        454        372        280        295
## SGK1              2867       3922       3148       2991       3074       3603
## IFNGR1            2525       3567       3303       3161       1966       2862
## TNFAIP3           3845       1630       2595       4641       6592      14267
## SOD2             46281      39191      44622      55227      39884      84406
## LPAL2               14          6         18         10          3         25
## PLG                  0          0          0          1          0          1
## CCR6                59         94        103         72         63         33
## RAC1              2632       3550       3438       3085       2628       2832
## ZNF316             798        730        663        567        647        776
## AHR                509        830        901        490        595       1445
## IL6                  8          3          4          4          3          2
## TOMM7             2160       1819       2136       2147       2677       1232
## CYCS               512        587        517        593        804        727
## AQP1                 3          1          5          0          3          0
## NT5C3A             740        978       1366        936        784        879
## EGFR                 0          0          0          0          0          0
## CD36              1642       3186       1889       1531       2287       2292
## SAMD9             1393       3848       3775       2341       1566       2509
## SERPINE1             5          4         18          9         11          6
## CUX1              1466       1781       1486       1565       1603       2035
## PSMC2              258        436        347        312        311        293
## NAMPT            48235      39070      53261      58323      38779      85285
## HYAL4                0          0          0          0          0          0
## LEP                  5         17          8          8          9          1
## CALD1                4          8         44         13          9         10
## BRAF               847        697        773        627        654        857
## EZH2                72         73         66         43         60         64
## DNAJB6            1321       1690       1647       1676       1311       1574
## CSMD1               15         28          2          1          0         16
## CTSB              3766       7076       4885       5627       4323       5330
## EGR3               175        638        466       1068        312       1567
## TNFRSF10A          176        131        148        111        124         90
## BNIP3L            1860       2839       2577       2406       1808       2535
## DUSP4               32         40         64        103         89         85
## NRG1                43        217        166         70        133         86
## RPL7              9166       8251       9163       8838      10838       5586
## IL7                  8         25         18         13         20         12
## GEM                  0          1          0          0          3          3
## MYC                738        639        864        699        543        233
## GPT                  4          4          4          1          0          0
## JAK2              1215       1116        939        957        971       1575
## CD274              132        197        220        223        192        372
## IL33                 0          0          0          0          0          1
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              0          0          2          3          2          0
## TTC39B             164        126        197        112        168         93
## IFNA1                0          0          0          0          0          0
## TEK                 39          5          5         56         12         14
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              193        212        205        232        247        183
## ANXA1             4659       6611       6981       5716       5523       7445
## ERP44             1134       1399       1367       1514       1455       1650
## ZNF483              43         18         38         15         32         21
## TNFSF15              4          1          1          5          4          5
## TLR4              7292       8273       7395       7251       4769       8115
## PTGS1              369        636       1418        781        952        504
## HSPA5             5762       5049       4719       6105       5915       6458
## FNBP1             3427       3571       4004       3577       2769       3456
## CARD9              154        238        120         86        125        118
## TRAF2              116        118        145         97         97         82
## CLIC3              103         98        169        110        103         87
## IL2RA              160        100        150        124         78         56
## GATA3              325        230        391        336        257        170
## VIM              16150      15884      17298      16297      14501      17763
## CREM               131        127        135        143        119        184
## DKK1                 0          0          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              614        760        978        740        695        937
## PRF1              1607       2901       5745       2039       1981       3408
## ZMIZ1             1973       3181       2626       2203       1656       2265
## IFIT3             2011      15323      17354      10871       9124       6621
## TALDO1            8799       9541       9408      12494       9027      10803
## IGF2                 0          0          1          0          0          0
## INS-IGF2             0          0          1          0          0          0
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1378       1405       1814       1358       1201       1260
## TRIM22            1627       4296       4690       3118       2723       4144
## PTH                  0          0          0          0          0          0
## SAA1                 1          0          0          0          1          1
## SLC1A2               3          0          1          3          1          2
## FOSL1               20         16         17         55         31        142
## CCND1                6          7         13          7          4          3
## JRKL               100         85         91         79         56         49
## MMP7                 0          0          0          0          0          0
## MMP1                 0          0          8          1          1          0
## MMP3                 0          0          0          0          0          0
## CASP1             2493       3090       2896       3409       2788       4338
## DLAT               172        237        195        163        172        139
## IL18                61        172         65         71         82         89
## CD3E              3417       1947       3148       3752       3952       1784
## MCAM               275        241        206        193        237        359
## WNK1              4575       4708       5035       4263       3358       4387
## TNFRSF1A          3640       4603       4725       4369       2730       4192
## GAPDH            15937      18868      15523      18561      18010      22887
## CD4               3390       5549       3737       4241       3717       3373
## SLC2A3           15074       6959       7787      10942       9408      18154
## CLEC4D             621        506        312        566        294       1082
## KLRB1              761        373       1289       1155        837        523
## CD69              1789        785        702       1354       3108       3060
## CLEC2B            1778       1468       1921       2152       1602       2817
## OLR1                21          3         15          7         10         11
## ABCD2              157        125        187        136        194        109
## LRRK2             9292       7817       9374       9783       6317      15071
## VDR                355        492        600        357        352        515
## TMBIM6           12559      15317      15040      16106      13010      15152
## PFDN5             2659       3130       3040       3265       3759       2423
## SP7                  0          1          0          1          0          0
## MUCL1                1          0          0          0          0          1
## CD63              2732       2655       2550       3308       2974       3647
## SUOX               974       1145       1180       1118        874       1304
## RPS26              596       4880        708        783        898        682
## RPL41             6345       6451       7071       7875       8965       4400
## IL23A               39         25         38         29         41         27
## DDIT3              728        401        372        478        350        791
## IFNG                39         15         34         39        131         82
## IL22                 0          0          0          1          0          0
## LYZ              80492     125208      52500      49393      77717      37750
## CAPS2                6          3          5          8          4          4
## SYT1                 4          7          1          1          7          5
## BTG1             10233       9433       8074      10181      10475      11260
## HCAR3             3405       1381       3599       3602       3877       5767
## GJB2                 1          4          0          0          1          6
## GJB6                39         13          4         18         34         71
## TNFSF11              4          0          1          2          1          0
## TPT1             51861      47618      50317      53125      60695      38202
## LMO7                91         59         73         62         52         32
## TNFSF13B          2458       3515       3603       3824       2611       3207
## LAMP1             2867       3028       2869       3063       2937       3229
## PSME2              934       1576       1427       1137       1548       1587
## GZMB               686       1046       1456       1050        946       1634
## RPL36AL           1898       2177       1902       2335       2757       1791
## PYGL              7717       4631       4976       6689       4655      11724
## HIF1A             1973       2465       2872       2051       1920       3886
## FOS              48833      52199      10706      71840     100052      56916
## JDP2               656        977        726        634        552        875
## NOXRED1              8          6         11          6          8         13
## SERPINA1         26150      26330      27619      31625      23412      36921
## CDC42BPB           186        331        223        172        139        184
## PLA2G4D              0          0          0          0          0          0
## TRIM69               7         31         14         11         19         16
## SLC51B               0          0          0          0          0          0
## SMAD3              570        613        720        558        565        339
## CYP1A1               0          2          2          0          0          1
## AKAP13            4547       5519       5141       3840       3688       6212
## MEFV              3084       3834       3427       3236       1924       3422
## SOCS1               64         54         58         86         68        118
## ATXN2L            1998       1787       1861       1760       1702       1501
## CD19                96        290        161         89        114         71
## ITGAL             5208       5155       6623       5841       5488       5761
## ITGAM             6329       5457       4940       6177       4591       8012
## ITGAX             5866       4514       5066       5176       4128       7309
## DNAJA2             650        724        581        597        531        652
## SIAH1              120        150        136         90        109        116
## ADCY7             2902       3249       2929       2285       2040       2520
## NOD2               403        679       1544        380        962        711
## CMTM2             2563       1802       1789       3614       2690       3580
## SF3B3              808        906       1031        799        880        752
## PSMD7              521        726        682        605        656        706
## WWOX                31         35         36         43         45         28
## MAF                424        405        551        414        478        420
## SLC7A5             172        307        170        412        214        209
## CXCL16            1514       2664       1569       2282       1631       3460
## XAF1               647       2287       2794       1414       1283       1056
## CD68              2483       5852       3188       3409       4021       3221
## PER1               385        435        443        469        467        763
## NOS2                 0          0          1          0          0          0
## TRAF4               82        147         85        104         78         70
## CCL2                 6        154         22         59         18         25
## CCL5              3250       1922       5942       5491       6940       3846
## CCL3               254        504        120        323        347        892
## CCR7               840        722        790        637        544        231
## STAT3             4894       5638       5620       4961       3646       6563
## SOST                 0          0          0          0          0          1
## ITGA2B             173        162       1421        589        517        278
## EFCAB13              9         23         30         10         20         14
## NPEPPS            1035       1029        937        847        698       1225
## TBX21              319        270        655        374        358        354
## COL1A1               0          0          0          0          0          0
## MRPS23             116        191        173        144        139        121
## MIR21                3          5          7          9          3          5
## RPS6KB1            382        388        441        313        329        284
## ACE                 59         36         41         47         31          9
## ERN1              1304       1030       1489       1164        889       1219
## PRTN3                5          8          2          4          0          6
## PLIN5              117        112         77        138         70        132
## RETN                54         44        216         34         79         48
## CCL25                0          0          1          0          0          0
## ICAM1             1395       1502       1417       2121       1894       3540
## TYK2              1701       2061       1793       1583       1214       1929
## SMARCA4            685        656        699        623        605        480
## ACP5               186        672        259        389        382        200
## JUNB             37761      26337      18348      49774      37584      32016
## CYP4F22             49          9         42         43         36         60
## JAK3              2206       1410       1986       1495       1534       2931
## JUND              7376       6399       3688       7954       9481       8295
## CEBPA              752        949        559        674        756        876
## CEBPG              205        313        269        219        220        227
## ACP7                 0          0          1          0          0          0
## ZFP36            22787      16942      10164      35867      36470      45945
## TGFB1             4805       4746       5724       5347       4435       5166
## RPS19             9117       8323       9109       8901      10456       5975
## PSG2                 0          0          0          0          0          0
## FUT2                 3          1          2          3          1          5
## NKG7              3087       2522       6181       5237       7096       4322
## ZNF415               7          7         26          5          3          3
## LILRB2            3877       5147       3993       4556       3699       4783
## LILRA5            2796       3628       2321       2847       2289       3573
## KIR3DL1             42         51        140         57         90          9
## KIR3DL2             30         54        120         28         14         10
## SMOX                46         65        280        129        147         53
## BMP2                22          4         18          8          5          5
## GINS1                7          8         14          5         14          8
## PLCG1              881        609        791        652        633        412
## YWHAB             5375       6365       5940       5737       5895       7457
## PI3               1183       1524       1933       1073       1586       2898
## MMP9              3789       1613       1226       1445       1745       6318
## CD40               125        261        149        103        126         83
## PFDN4               35         44         65         43         49         47
## BMP7                 0          0          0          0          0          0
## RPS21             4186       3712       3981       4165       5521       2488
## MX1                544       6305       7286       4480       3169       1695
## PFKL              1003       1370       1097       1022        962        887
## IL17RA            6657       6493       5748       6354       4610       8184
## UBE2L3             903       1132       1160       1059        970       1068
## TPST2             1102        895       1434       1353       1321       1149
## XBP1               743       1212       1094        978        804        917
## UQCR10             426        577        527        613        613        499
## SEC14L2             66         35         26         22         30         15
## APOL6             1262       2096       2568       1399       1465       2340
## APOL1              537        810        804        899        784        999
## TYMP              2958       6644       3796       4225       4051       3399
## BEND2               15         12        110         35         97         15
## PHEX                 7          4          8          5         15         15
## TIMP1             1504       1526       1424       1531       1250       1827
## FOXP3               84         89         67         98         94         66
## MSN              23913      24737      27901      29904      26490      29191
## PGK1              7390       7707       6845       8455       8412       9688
## LAMP2             7222       7687       7571       8039       5767       8886
## CD40LG             163         99        191        194        109         46
## IRAK1             1310       1523       1251       1267       1382       1416
## COX2             41656      51261      45220      47337      62463      35140
##             GSM3308467 GSM3308468 GSM3308469 GSM3308470 GSM3308471 GSM3308472
## TNFRSF9            126        117        153        120        117         95
## ENO1              6828       3846       4229       7213       6318       5957
## PIK3CD            5447       5877       5368       6406       5104       3327
## PGD               4514       4103       4968       5792       5069       3192
## MTHFR              552        347        523        373        511        367
## TNFRSF1B         12429      11876      13734      12283      13535      11435
## PINK1              580        577        843        746        586        528
## IFNLR1              86         55         28         25         59         73
## RUNX3             4682       2618       4416       3269       2866      10497
## SH3BGRL3         10737       8976       9497      13765       9429       9835
## CD52              5033       2097       2376       3994       3097       5247
## IFI6              6406       4578       1032        370       1711        763
## ZC3H12A            501       1468       1409       3438        718        660
## UTP11              112         32         43         59         56         67
## JUN               7397      23010      43554      12353      25317      32756
## KANK4                0          0          0          0          0          0
## EFCAB7              24          8         17         10         12         23
## IL23R                1          0          0          0          2          3
## ADGRL2               0          0          0          0          0          0
## GBP3               461        191        202        130        224        131
## GBP1              1780       1604        959        201       1642        365
## GBP5              3139       5383       3454       1068       5623       1603
## TGFBR3            1231        596        681        470        624       1605
## VCAM1                5          0          9         12          0         11
## PTPN22             519        201        293        228        257        371
## CD160              298         90        120         62         81        139
## FCGR1A            1061       1626        849        581       1652        307
## MCL1             22516      43784      54334      32861      27603      20207
## CTSK                78         56        105         85         93         32
## RORC                42         18         37         15         19         46
## S100A9          124763     155767     128974     225091     105031      59677
## S100A12           4436       5269       5015       6801       4394       1241
## S100A8           44018      62735      51139      89867      45173      20690
## IL6R              3441       3229       3385       3095       3591       1996
## RIT1              1165       2008       1532       1896       1192        940
## BGLAP                7         11          4         10          6          6
## IFI16             4242       1838       1333        907       1869       1055
## AIM2               143        138        102         66        164         47
## CRP                  0          0          0          0          0          0
## FCGR2A           10671      11862       9917      11013      10986       5285
## HSPA6             1357       1536       1205       1277       1299        610
## FCGR3A           19021      18009      14137       8487      18251      10677
## SELL             35711      31871      41725      27774      30148      17656
## GLUL             14050      18911      14725      13028      13269       9963
## PTGS2            14882      17881      14396       6529       8739       2923
## CRB1                 1          1          0          1          1          0
## KDM5B              423        610        799        583        442        351
## IL10                12          8          7         16          4          6
## YOD1               172        187        370        354        212        179
## HHAT                55         32         22         35         31         65
## TRAF5              353        196        246        211        285        316
## NLRP3             1070        821       1081       1018       1447       1083
## LINC01250            0          0          0          0          0          0
## RPS7              9329       4948       6277      10473       8128      10458
## RSAD2             7504       3927        342         56        934        132
## FOSL2             3340       7776       5537       5180       4065       8138
## REL               1094       1049       1292       1048       1163       1141
## TGFA               331        572        410        464        403        202
## DYSF              4253       7096       5394       4949       5263       2152
## HK2                975       1112       1451       1034       1337        562
## CD8A              3735       1125        623       1520       1004       5363
## CD8B              1502        554        416       1334        368       1656
## EIF5B              589        290        336        353        487        473
## IL1R1              184        377        479        400        217        190
## RGPD6               67         61         83         66         58         85
## IL1A                 3          8         13          9          2          2
## IL1B              2823       2209       2437       3780       1797        363
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             4112      10007       5963      16721       3984       1005
## NMI               1706        967        922        977        997        602
## TNFAIP6            801        637        569        273       1143        247
## IFIH1              825        697        509        313        582        246
## SCN1A                0          0          0          0          0          0
## ABCB11               0          1          3          1          2          0
## RBM45               63         23         28         37         42         50
## FRZB                 0          0          0          0          0          0
## TFPI                11          1          5          5          1          4
## STAT1             6817       4126       3793       1848       5392       1926
## NABP1              512       1110       1394        475        966        330
## SF3B1             4249       4165       4757       4240       4020       3500
## CASP10             374        224        374        223        427        334
## CD28               723        501        541        792        431        564
## CTLA4               94         58         63         70         66         66
## ICOS               263        294        112        358        146        201
## NDUFS1             674        246        289        323        353        363
## CXCR2            13559      11526      17491       8640      10358       7005
## IRS1               192         75         74         46         66         41
## CCL20                1          6         18         12          0          6
## ATG16L1            286        251        282        300        309        383
## GPR35               79         85         94        129         98         99
## PDCD1               90         24         33         49         21         91
## PPARG                9          4          5         13          4          1
## RPL15            15294       7584      10617      16786      13302      15961
## EOMES              296         49        121         93         74        209
## CX3CR1            2673        286        462        391       1563        365
## ACKR2                1          4          0          0          0          0
## CCR2               933        124        351        441        540        128
## CCRL2               74         35         37         50         72         28
## TLR9                57         51         91         68         51         38
## ARHGEF3           1605        923       1227       1009       1157       1012
## ADAMTS9              0          0          0          0          0          0
## TMEM45A              1          1          0          1          0          3
## CD80                14          7          3          3          7          9
## CD86               935        354        532        516       1025       1119
## MIX23               25          7         16         15         19         29
## PLS1                10         11         23          9          8         17
## PTX3                62         92        141        216        206         45
## GOLIM4              86         28         69         35         81         69
## MYNN               323        338        406        330        360        318
## TNFSF10           4724       2223       1561       1607       2136        606
## ADIPOQ               0          0          0          0          0          0
## SPON2             1159        464        984        141        435       2010
## S100P             2783       4807       4862       7023       1814       2013
## WDR1              6270       3755       3829       4551       4689       4929
## CD38               395        179        181        101        209        324
## PPARGC1A             1          3         10          2          0          6
## TMPRSS11B            0          0          2          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  1          0          0          0          0          0
## CXCL8            31577     142856     229948      93583      82191      24395
## CXCL2               65         81         82        103         40         14
## AREG                38        133       2145        822        195        695
## CXCL10              60         17         12          3         52         11
## CXCL13               7          0          1          0          0          1
## SPP1                53         16         45         58         83         32
## HERC6              572        280        107        100        162        136
## NFKB1              902        741        849        906        892        683
## SEC24B             380        399        532        422        441        388
## EGF                 44         24         10        101         10         18
## IL2                  0          0          0          1          0          0
## IL21                 3          0          1          0          2          1
## IL21-AS1             6          0          1          1          1          0
## SLC7A11             11         20         10         14         29          7
## IL15               145         34         56         49         89         72
## EDNRA                0          0          0          0          0          0
## TLR2              2998       4129       8510       5582       3308       1422
## FGB                  0          0          0          0          0          0
## DDX60             1622        868        311        127        502        177
## SPCS3             2380       1058       1460       1779       1607       1490
## TLR3                22         12         13          9         10         20
## OSMR                22         42         41         31         30         14
## GZMK               835        612        546        502        434       2013
## GZMA              2446        704        894        595        865       2256
## ANKRD55             40         38         66         38         78         38
## CENPK               26         28         65         55         20         90
## CAST              2837       2059       1811       2026       2320       2845
## ERAP1             2202        638        909        745       1125       1275
## ERAP2              169       1794        279       1765       1731       1626
## TNFAIP8           1457        725        921        886       1083        819
## CSF2                 1          1          0          0          0          2
## IL5                  1          0          0          0          0          0
## IL13                 1          1          0          1          0          2
## IL4                  3          2          1          0          4          1
## CD14             10050       5701       6017       8446       8454       5375
## CSNK1A1           1807       1179       1251       1421       1431       1104
## PPARGC1B           119         61        159        107        215         77
## TNIP1             4838       5071       4161       5643       4912       3090
## ATOX1              204        117        169        192        166        203
## FAXDC2             186        110        124        273        152        155
## IL12B                0          2          2          0          0          0
## MIR146A              0          0          0          0          0          0
## PDLIM7            1117       2172       1804       1991       1349        944
## SERPINB1          4499       3646       4458       5285       4082       3184
## SSR1              2602       1477       1628       1837       1992       1740
## CD83               710       1795       1437       1554       1552        588
## SOX4               106         64        154        116        256        204
## CMAHP               99         69         83         58         90         91
## HLA-A            45640      43315      43164      43202      38993      47557
## HLA-C            74176     106002      88929      70934      61996      59129
## HLA-B           105335     121942     118300      87553      94441      88479
## MICA               146         87        137        138        190         99
## LTA                 82         50         35         39         47         31
## TNF                168        193        153        251        390        219
## HLA-DRB1          4890       2982       3114       4849       7022       6455
## HLA-DQB1          2472       1392        772       3092       1525       3624
## PPARD              254        204        243        320        219        269
## CCND3             4605       3717       7781       4734       4146       5538
## VEGFA              163        221        210        348        258        317
## RUNX2              457        391        882        649        374        343
## IL17A                0          0          0          0          0          0
## IL17F                0          0          0          0          0          0
## PRDM1             1378        670       1378       2938        547       1164
## ATG5               420        259        328        370        361        394
## TRAF3IP2           157         98        202        175        144        162
## NCOA7              937        272        373        307        302        276
## SGK1              5463       4446       2614       3517       3823       1232
## IFNGR1            2074       1632       2872       2244       2279       1379
## TNFAIP3           3579      22245      42595      53001      10065      14273
## SOD2             31081      43768      41442      40803      50478      22592
## LPAL2               21          7         23         10         10         28
## PLG                  1          0          2          0          0          1
## CCR6                83         48         81         35         58        133
## RAC1              2856       1718       1633       3039       2499       1952
## ZNF316             590        883        684       1400        567        681
## AHR               1047        948       1890       1170       1833        768
## IL6                  1         21          7          6         19          4
## TOMM7             1764       1382       1810       2897       2494       2827
## CYCS               982        606        902        725        862        909
## AQP1                 2          1          2          6          3          0
## NT5C3A            1107        715        509        524        694        482
## EGFR                 0          0          0          0          0          0
## CD36              3067       1359       1144       2332       3281       1009
## SAMD9             3464       2321       1641        549       1731        774
## SERPINE1            14         15         17         17         19          9
## CUX1              1691       1559       1691       1903       2125       1611
## PSMC2              432        150        234        278        322        292
## NAMPT            38029      54930      52721      61809      43974      21114
## HYAL4                0          0          0          0          0          1
## LEP                  2          2          3          2          2          0
## CALD1               36          5          7         32         18         13
## BRAF               658        594        798        672        657        510
## EZH2                96         47         64         39         71         68
## DNAJB6            1106       1270       1235       1579       1218       1171
## CSMD1                7          0          1          0         21          1
## CTSB              5765       2594       3671       5670       5794       4771
## EGR3              1165       1335        741        581        492        108
## TNFRSF10A          134        133        127        148        105         92
## BNIP3L            2070       1338       1498       2130       1810       1049
## DUSP4               91        146        128         75         56        291
## NRG1               158        135         56        243        204         69
## RPL7             10713       5786       7433      13099       9451      10603
## IL7                 22          6         10          6          7         11
## GEM                  2          4          4          0          1          3
## MYC                920        316        387       1067        281        475
## GPT                  3          0          1          2          2          8
## JAK2              1112       1006       1524       1006       1247        657
## CD274              248        233        131         65        272         72
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              2          2          0          1          1          2
## TTC39B             146        114        156         83         91        179
## IFNA1                0          0          0          0          0          0
## TEK                  6         36         73         51         27         14
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              261        113        141        202        203        290
## ANXA1             7536       3346       5904       7427       7518       7929
## ERP44             1416       1178       1268       1065       1460       1077
## ZNF483              44         16         32         51         20         35
## TNFSF15             16          3          6          3          9          4
## TLR4              6398       5075       6919       3098       6019       2654
## PTGS1              689        709        658       1068        724        453
## HSPA5             5605       6432       6402       5323       5157       7013
## FNBP1             3436       1943       2426       2509       2407       2703
## CARD9              195         90        142        126        192        158
## TRAF2              149         65        104         98         77        106
## CLIC3              104         56        150         37         53        366
## IL2RA              280         48        137        100        111        115
## GATA3              412        171        296        284        185        434
## VIM              16786      13791      11956      22450      14853      16144
## CREM               134        162        198        181        145        436
## DKK1                 0          0          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              866        716        795        963        650        641
## PRF1              5288        717       2343        525       1361       4129
## ZMIZ1             2250       2336       3080       2679       2197       1981
## IFIT3            21679      19009       3558        702       8494       1363
## TALDO1            6608       6710       7858       8515       7219       4825
## IGF2                 0          0          0          0          0          1
## INS-IGF2             0          0          0          0          0          1
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1517        928       1181       1128       1152       1430
## TRIM22            5743       3605       2341       1179       3010       1400
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          1          0          0          1
## SLC1A2               0          6          2          4          4          0
## FOSL1              130        283         87        172         79         55
## CCND1                7          6          9          4          4          4
## JRKL                99         32         73         30         83         51
## MMP7                 0          0          0          0          0          1
## MMP1                 2          0          1         18         11          0
## MMP3                 0          0          0          0          0          0
## CASP1             3183       1993       2290       1729       3063       1594
## DLAT               234         68         85         82        130        171
## IL18               100         27        130        145        117         71
## CD3E              4042       1826       1726       2962       2144       4109
## MCAM               204        185        324        253        274        202
## WNK1              4306       3218       4345       3255       3037       3146
## TNFRSF1A          3130       2332       2704       1775       2713       1437
## GAPDH            19212      15522      15500      30598      19052      20914
## CD4               3908       1641       2252       1936       3672       3401
## SLC2A3            8458      19415       7925      14584      11219       8951
## CLEC4D             394        390        871        259        496        223
## KLRB1              878        583        736        306        723       1363
## CD69              3161       6225       7577       5674       3819       3330
## CLEC2B            2013       1877       1361       2147       1642        957
## OLR1                11         23         16        207          5          5
## ABCD2              239        121        144        142        171        122
## LRRK2             5556       8094       9950       6048       7660       2936
## VDR                333        429        449        429        225        270
## TMBIM6           13663       9729      11960      10223      12505       9383
## PFDN5             3613       1823       2433       4439       3606       3737
## SP7                  0          0          0          0          0          0
## MUCL1                0          0          2          0          0          0
## CD63              2978       3243       3840       5039       3207       2256
## SUOX               966        531        905        735        775        644
## RPS26              831       2348       2763       8188       3166       4172
## RPL41             8860       4656       5425      10038       7228       9371
## IL23A               35         21         19         23         25         33
## DDIT3              350        970        831        801        479        322
## IFNG                80         96        161         42         53         76
## IL22                 2          3          2          6          0          0
## LYZ              81699      23110      57089     131163     139099      28887
## CAPS2                4          0          7          3          9          2
## SYT1                 5          0         11          2          1          0
## BTG1              8218      12034      17778      11739      11676      17118
## HCAR3             2591       6388       6922       3580       5229       1757
## GJB2                 1          6          2          0          4         11
## GJB6                15         91         25         29         16         62
## TNFSF11              4          0          6          5          5          3
## TPT1             61663      34093      39686      77239      53955      57853
## LMO7                59         39         44         53         57         39
## TNFSF13B          4056       3012       1388       1130       2030       1500
## LAMP1             2746       2396       2554       2706       2827       2452
## PSME2             1649        979       1038        906       1751       1293
## GZMB              1732        638       1528        299       1060       2880
## RPL36AL           2829       1867       1895       3269       2263       2170
## PYGL              3331       5143       3809       5737       4603       1941
## HIF1A             2071       4514       4666       4197       3335       2362
## FOS              38016     129899     180469      60580     110134      72375
## JDP2               570        936       1794        954        569        858
## NOXRED1             13         13         25          6          4          8
## SERPINA1         22907      22277      22443      23936      25192      13797
## CDC42BPB           221        135        185        218        244        248
## PLA2G4D              0          0          0          0          0          0
## TRIM69              24         14         13         22         14          4
## SLC51B               0          0          0          0          0          0
## SMAD3              673        402        451        445        587        789
## CYP1A1               0          0          0          1          1          1
## AKAP13            4076       4765       5992       4443       4738       4441
## MEFV              2115       1585       1828       1802       1757       1038
## SOCS1              166        112        213        249        149        229
## ATXN2L            1737       1153       1457       1604       1411       1776
## CD19                97         98         27         30        156        104
## ITGAL             6973       4475       4477       4143       5355       6175
## ITGAM             5037       5736       5165       6317       5400       3696
## ITGAX             3396       6288       8472       4825       6153       2866
## DNAJA2             643        503        694        643        515        553
## SIAH1              105        105        168        102        100         95
## ADCY7             2780       1858       2334       1572       2513       2345
## NOD2               847        509       1068        456       1169        373
## CMTM2             1490       2863       2492       2324       2090       1312
## SF3B3             1099        497        680        498        805        771
## PSMD7              724        522        571        891        652        675
## WWOX                46         32         34         35         33         43
## MAF                781        338        445        280        471        936
## SLC7A5             489        569        465        795        290       1012
## CXCL16            1339       2552       3025       2625       2604       2982
## XAF1              2978       1690        703        208       1163        534
## CD68              3757       2023       2243       3111       4470       3535
## PER1               405       1260       6195       3279       1324       2932
## NOS2                 1          3          3          1          4          0
## TRAF4               76         93        104         77         99        174
## CCL2               143         15          2          2         32          0
## CCL5              8175       3240       3236       3370       3606       9635
## CCL3               550        505        811        743        623        249
## CCR7               484        422        497        596        554        296
## STAT3             3934       3591       3855       3616       3147       2205
## SOST                 0          0          0          0          0          0
## ITGA2B             816        557        155       2363        412        307
## EFCAB13             15         22         24         13         21         23
## NPEPPS             682        652        985        646        742        454
## TBX21              588        219        428        134        321        698
## COL1A1               0          4          3          1          1          1
## MRPS23             180         56         57        108         98        132
## MIR21                5          3          8          3          1          2
## RPS6KB1            407        251        311        248        356        330
## ACE                 93         26         66        102         50         75
## ERN1              1138        887       2284       1277       1139       1547
## PRTN3                6         39        120        658          2          3
## PLIN5               53         99        174        102         85         57
## RETN                55         99        108        685         26         78
## CCL25                3          0          0          0          2          0
## ICAM1             1783       4956       3556       7201       2948       1358
## TYK2              1461       1419       1779       1243       1344       1029
## SMARCA4            697        426        468        578        489        729
## ACP5               435         98        117        310        218        352
## JUNB             25660      40126      46069      55661      25190      43285
## CYP4F22             58          9         40          8        174         64
## JAK3              1740       2383       2689       2121       1657        975
## JUND              7252      19504      24436      15588      12742      17190
## CEBPA              634        461        480        809        912        483
## CEBPG              303        151        217        234        228        255
## ACP7                 0          0          3          0          1          1
## ZFP36            23714      61947      75564      68643      30266      24067
## TGFB1             5145       4460       3736       6595       3596       5147
## RPS19            11647       5935       7458      15408       9277      13824
## PSG2                 0          0          0          0          0          0
## FUT2                 2          3          3          2          1          2
## NKG7              9727       3503       4595       3300       3719       9679
## ZNF415               6          2         14          0          9          3
## LILRB2            4166       4704       5567       4144       4741       4459
## LILRA5            2870       3464       1448       2750       2519       2776
## KIR3DL1            112         15        101         23         39        225
## KIR3DL2             39         16         53         14         20        137
## SMOX               103         81         94        169         60         93
## BMP2                 5         20         10         20          4          1
## GINS1               14          4          4         10          8         10
## PLCG1              810        442        609        559        510        589
## YWHAB             6006       4317       3943       4992       5708       5028
## PI3                856        916       3227       1245       1059        614
## MMP9              2589       3614       3374       4861       2265       1404
## CD40               249         56         46         82        190        165
## PFDN4               48         35         41         63         42         58
## BMP7                 0          0          0          0          0          0
## RPS21             5230       1642       3303       6620       4138       6035
## MX1               7605       2209        965        209       1687        508
## PFKL              1365        561        760        760       1053       1232
## IL17RA            4467       5129       5735       5994       4658       2581
## UBE2L3            1189        566        612        914        769        840
## TPST2             1776       1087       1435       1576       1005       1748
## XBP1              1669        610        956       1353        756        998
## UQCR10             684        350        388        542        477        492
## SEC14L2             29         26         24         52         24         38
## APOL6             2547       2205       1468        669       1883       1048
## APOL1              913        681        643        281        858        462
## TYMP              4398       3091       2874       2645       4900       3120
## BEND2               40         48         47         50         43         46
## PHEX                10          8          3          3          7          6
## TIMP1             1692       1083       1896       2057       1262       2038
## FOXP3              177         36         53         36         49        113
## MSN              23061      19501      21320      22699      21471      19838
## PGK1              7355       7067       7108       8866       8917       7076
## LAMP2             5972       5917       7682       5933       5607       3225
## CD40LG             137         38         92         48         83         88
## IRAK1             1374       1129       1483       1690       1440       1550
## COX2             57762      34006      35662      68548      46658      71560
##             GSM3308473 GSM3308474 GSM3308475 GSM3308476 GSM3308477 GSM3308478
## TNFRSF9             49         68         69        107        111         68
## ENO1              7354       3626       6669       5434       6071       6647
## PIK3CD            6613       6162       5760       5003       7728       6213
## PGD               7186       8038       3806       4271       5972       5718
## MTHFR              365        157        520        414        487        336
## TNFRSF1B         16274      12808      14304       9864      15244      14301
## PINK1             1047        978        601        642        838        947
## IFNLR1              60         13         48         51         40         48
## RUNX3             4051        968       2757       2250       2656       4036
## SH3BGRL3         13114       8673       8598       6741      10969      10870
## CD52              3728       1391       4954       2744       3523       3789
## IFI6              1756       1910       5111       1439        910       5129
## ZC3H12A            324        493        483        630        648        530
## UTP11              123         54         86         56         61         85
## JUN                333       2622       3712       8215      15481       8201
## KANK4                0          0          0          1          0          0
## EFCAB7              22         13         25         31         18         22
## IL23R                1          0          3          0          8          0
## ADGRL2               0          0          0          0          0          0
## GBP3               200         45        276        217         64        203
## GBP1              1798       1691       2341        658        529       1583
## GBP5              3845       4726       6616       2281       1427       3839
## TGFBR3             965        184        439        342        444        748
## VCAM1                1          2          0          2          0          2
## PTPN22             475        207        256        242        246        333
## CD160              225         23        114         83        114        126
## FCGR1A             718       1947       2805        539        654        889
## MCL1             17357      34811      20459      21450      28531      26941
## CTSK                29         18         66         45         44         65
## RORC                42          2         57         23         45         30
## S100A9          112504     243670     117314      95407     140171     102096
## S100A12           3336       9862       2895       3653       3469       3632
## S100A8           38854      99115      41982      38585      50907      33455
## IL6R              5694       4394       3796       3596       5035       3901
## RIT1              1253       2053       1217       1178       1667       1430
## BGLAP                8          4          8          5          3          5
## IFI16             3532       4139       5206       1478       2078       3922
## AIM2               147        437        363         64         96        235
## CRP                  0          0          0          0          0          0
## FCGR2A           13784      18369      16411       8214      16892      11982
## HSPA6             5145       2076       2632       1201       2237       2446
## FCGR3A           27644      19946      23202       7325      17207      23682
## SELL             41107      69050      35846      29377      37359      53257
## GLUL             12178      26637      12482      12174      16274      13963
## PTGS2             3225       8573       2584      19954      14919       9108
## CRB1                 0          0          2          0          0          0
## KDM5B              416        438        404        457        495        452
## IL10                 1          9         11          4          0          6
## YOD1               191        297        325        237        186        295
## HHAT                36         12         51         32         27         27
## TRAF5              251         94        333        328        291        285
## NLRP3              811        425        808        897       1188        709
## LINC01250            0          0          0          0          0          0
## RPS7              8152       3299      10294       6429       6784       7915
## RSAD2              912       1671       6570       1100        261       4803
## FOSL2             2946       5654       2801       3750       4697       3156
## REL                945        796       1204       1198       1060       1096
## TGFA               523       1376        441        370        540        493
## DYSF              4759       9430       4772       4078       5135       5125
## HK2               1069       1066        737        822        861        841
## CD8A              1895        347       1200        553        644       2344
## CD8B               613        131        927        504        303        944
## EIF5B              512        151        468        330        331        470
## IL1R1              166        637        136        279        285        304
## RGPD6               68         34         77         64         49         70
## IL1A                 0          0          0          2          1          0
## IL1B               431        288        680       1379       1425        597
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             3236       3287       3733       3393       3739       3984
## NMI               1903       2868       2132        869       1300       2199
## TNFAIP6            650       1044        820        576        266        435
## IFIH1              522        394       1025        377        305        734
## SCN1A                0          0          0          0          0          0
## ABCB11               0          0          0          1          1          2
## RBM45               68         24         63         44         61         54
## FRZB                 0          0          0          0          0          0
## TFPI                20          9          5          3          3          6
## STAT1             5697       5164       6476       2717       2894       5931
## NABP1              437        911        563        862        721        503
## SF3B1             3923       3565       3741       3326       3721       3993
## CASP10             340        208        381        354        330        411
## CD28               498         99        846        484        489        561
## CTLA4               34         24         93         47         58         48
## ICOS               143         48        240        102        122        110
## NDUFS1             556        299        539        363        420        553
## CXCR2            27876      25659      17658       9896      22239      14826
## IRS1                44         41         92         96         72         85
## CCL20                1          2          2          3          2          3
## ATG16L1            212        102        277        253        257        293
## GPR35               91         42        112         88        110        134
## PDCD1               41         13         31         27         19         33
## PPARG                6          5          6          0          1          2
## RPL15            14669       4770      16737      10675      11342      12893
## EOMES              263         20         50         85         78        143
## CX3CR1            2630        164       1321        747        847       1664
## ACKR2                2          0          0          1          0          0
## CCR2              1182        234        763        432        592        756
## CCRL2               35         25         71         34         42         23
## TLR9                94         70         62         69         56         40
## ARHGEF3           1043        362       1362        949       1027       1369
## ADAMTS9              0          0          0          0          1          0
## TMEM45A              3          2          2          1          3          1
## CD80                 2          2          5         16          4          5
## CD86              1111        330        973        526        898        796
## MIX23               31          9         38          7         23         20
## PLS1                26          4         15         12          7         21
## PTX3                39         54         81         96         69         55
## GOLIM4              96         36         78         68         75         95
## MYNN               277        331        311        308        372        318
## TNFSF10           4272       3482       5128       1862       2336       4621
## ADIPOQ               0          0          0          0          0          0
## SPON2              890        165        426        152        505        904
## S100P             3650       4493       1238       1436       4145       3473
## WDR1              8241       5378       4763       3604       5561       6750
## CD38               403        256        293        197        176        283
## PPARGC1A             2          3          0          3          6          0
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          0          0          0          0
## CXCL8            13960      34386      13415      83592      95007      35672
## CXCL2                0          4          6         43         42         33
## AREG                 3        141         21         44         20         61
## CXCL10              44          7         65         13         20         34
## CXCL13               1          3          1          0          0          0
## SPP1                21        189         19         49        157          5
## HERC6              199        110        322        160        156        341
## NFKB1              942        573        890        642        698        783
## SEC24B             535        410        390        355        398        483
## EGF                 91         35         47          7         22         87
## IL2                  0          0          0          0          0          0
## IL21                 1          1          0          0          0          1
## IL21-AS1             2          1          1          0          2          2
## SLC7A11             25         15         11          9         19          6
## IL15                88         42         69         58         42         85
## EDNRA                0          0          0          0          0          0
## TLR2              3642       9907       4376       3165       3471       4930
## FGB                  0          0          0          0          0          0
## DDX60              499        516       1437        499        260       1100
## SPCS3             2393       1758       1984       1454       1682       1945
## TLR3                22          0          7          5          5         13
## OSMR                25         39         31         30         23         38
## GZMK               605        199        407        351        337        487
## GZMA              1582        306        679        510        804       1208
## ANKRD55             84         53         86         56         47         85
## CENPK              104         30         91         48         50         73
## CAST              3233       1265       2581       2389       2428       2483
## ERAP1             1740        658       1442       1134       1128       1435
## ERAP2              125       1607       3433       1132       1098       1892
## TNFAIP8           1579        697       1348        986       1096       1382
## CSF2                 1          0          0          0          0          0
## IL5                  0          0          0          0          0          3
## IL13                 0          1          0          0          0          1
## IL4                  4          1          2          2          3          1
## CD14              7491       6696       8639       6183      12078       8719
## CSNK1A1           2047       1337       1737       1063       1506       1575
## PPARGC1B           100         47        226        150        132        202
## TNIP1             4920       5616       5068       3665       4911       4563
## ATOX1              232        141        152        147        157        211
## FAXDC2             372        110        246        105        137        324
## IL12B                1          1          3          2          2          1
## MIR146A              0          0          0          0          0          0
## PDLIM7            1747       2073       1393       1261       2123       1740
## SERPINB1          4269       7121       5405       3405       5450       4206
## SSR1              2717       1931       2489       1417       1858       2285
## CD83               304        111        626        846        851        336
## SOX4               117        106        172        130        127        239
## CMAHP               79         35         93        106         61         81
## HLA-A            55916      46739      49914      30731      39581      44376
## HLA-C            82558     110779      79036      77176      88307     110753
## HLA-B           109125     125402     129118      79308      91627     107900
## MICA               128         37        168        122        138        131
## LTA                 59          5         79         42         57         52
## TNF                139         59        193         68        156        287
## HLA-DRB1          2900       1541       3385       4618       3236       3490
## HLA-DQB1           388        157        479        883       3618       2465
## PPARD              217        115        340        242        260        263
## CCND3             4899       5716       3860       3033       3176       6251
## VEGFA              110         92        165         96        143         98
## RUNX2              399        551        456        394        433        538
## IL17A                0          0          0          0          0          0
## IL17F                0          0          0          0          0          0
## PRDM1              699        694        630        333        390        778
## ATG5               462        258        357        294        329        464
## TRAF3IP2           185         89        232        153        144        188
## NCOA7              388        237        464        272        221        303
## SGK1              3520       1156       2349       1870       3172       3004
## IFNGR1            4078       4628       2724       1444       2837       2776
## TNFAIP3           1537       9256       4021       6176       5102       4740
## SOD2             41661      68419      43488      31642      47692      32125
## LPAL2                7          3          9         16         14         17
## PLG                  0          0          0          1          0          0
## CCR6                75         23         92         79         72         41
## RAC1              3471       2140       2375       1647       3438       2832
## ZNF316             694        511        728        543        849        788
## AHR                467        504       1338       1239        992        871
## IL6                  0          0          5          6          2          7
## TOMM7             1878        777       2693       1727       1499       2171
## CYCS               577        268        644        480        687        684
## AQP1                 0          2          5          6          4          6
## NT5C3A            1131       1031       1137        620        555       1183
## EGFR                 0          0          0          0          0          0
## CD36              2287        809       3475       1795       2481       2394
## SAMD9             1855       2050       2969       1773       1370       2923
## SERPINE1            13          3         12          6         11         19
## CUX1              1537       1619       1542       1246       1834       2009
## PSMC2              446        161        313        222        286        372
## NAMPT            43789     104711      56383      30419      57487      47580
## HYAL4                0          1          0          0          0          0
## LEP                 15          0          5          0          3          3
## CALD1               40         11         11          2         21         41
## BRAF               543        566        645        629        649        723
## EZH2                55         34         53         67         57         47
## DNAJB6            1768       1682       1139        740       1421       1472
## CSMD1                0          1          6          1          2          2
## CTSB              6130       4086       7994       4045       4494       5136
## EGR3               227        455        330        498        941        497
## TNFRSF10A           99         41        227        143        118        161
## BNIP3L            2560       2407       2108       1623       2570       2152
## DUSP4               28         33         39         38         49         14
## NRG1               140         89         95        142        113         55
## RPL7              9400       3228      12142       7281       7598       9173
## IL7                 11          8         13          9         11          8
## GEM                  0          1          0          2          2          0
## MYC                608        195       1106        282        329       1146
## GPT                  2          0          3          0          1          0
## JAK2              1127       1188       1171        904       1027       1193
## CD274              164        379        723         72        133        182
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              8          0          1          0          1          3
## TTC39B             109         48        212        171        110        169
## IFNA1                0          0          0          0          0          0
## TEK                 13         20         26          4          8         16
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              237         86        237        138        178        196
## ANXA1             4753       5041       5306       5802       6248       6309
## ERP44             1389       1400       1399       1046       1236       1412
## ZNF483              17          3         38         34         27         31
## TNFSF15              7          5          6         16          8          1
## TLR4              7552      12677       6100       4645       8786       6073
## PTGS1             1913        517        778        404        690       1613
## HSPA5             4742       4746       4237       6889       5164       5133
## FNBP1             4355       2739       3372       2249       2890       3672
## CARD9              193         71        164         99        165        174
## TRAF2              134         44        116         84        106        118
## CLIC3              264         32         62         76        147        149
## IL2RA               96         28        144         65         91        106
## GATA3              309         62        301        219        304        229
## VIM              15799      13074      16462      13965      19218      19685
## CREM               172        206        174        129        139        152
## DKK1                 0          0          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              928        695        664        650        666        830
## PRF1              3881        632       1288       1079       1683       3332
## ZMIZ1             1884       1570       2251       1683       2431       2650
## IFIT3             5933       7585      20598       4748       2786      19276
## TALDO1           12172      12953       7335       6079      10157       8385
## IGF2                 1          0          0          0          1          0
## INS-IGF2             1          0          0          0          1          0
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1617        824       1177        894       1230       1581
## TRIM22            2998       6824       5813       2252       1820       6133
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          1          0          0          0
## SLC1A2               0          4          2          1          0          2
## FOSL1                5         34         35         64         73         34
## CCND1                3          3          4          4          7          6
## JRKL                90         28         91         75         61         54
## MMP7                 0          0          0          1          0          0
## MMP1                 1          2          7          0          2          4
## MMP3                 0          0          0          0          0          0
## CASP1             3243       4032       3990       2037       2557       3274
## DLAT               197         63        215        114        149        179
## IL18               121         76        113         79        108         74
## CD3E              3016        601       3892       1881       2151       3085
## MCAM               220        190        244        256        245        255
## WNK1              4294       2403       3718       2698       3500       4103
## TNFRSF1A          4509       4112       4116       2039       4483       3486
## GAPDH            16554      16366      18568      15341      18327      17603
## CD4               3642       1356       5188       2149       3466       3175
## SLC2A3            6167      16274       8675       6853      10485       9781
## CLEC4D             288       1209        256        467        478        605
## KLRB1             1258        409        950        499        605        779
## CD69               385        602       1805       2184       2182       2411
## CLEC2B            1828       1943       2530       1433       1674       1646
## OLR1                21          8         23         59         15          7
## ABCD2              128         34        212        152        120        188
## LRRK2            10297      11579       6698       7091       7937       9576
## VDR                753        389        446        404        373        365
## TMBIM6           15902      13164      11897       8424      13691      13502
## PFDN5             3326       1661       3804       2491       2955       3272
## SP7                  0          1          0          0          0          0
## MUCL1                0          0          0          0          0          0
## CD63              3172       3431       2679       1932       2767       2801
## SUOX              1296        954        872        779       1059       1016
## RPS26             3423        454       7623       2566       2765       3501
## RPL41             7238       3207       8737       5747       6196       7133
## IL23A               17         11         38         26         33         43
## DDIT3              350        639        537        607        713        614
## IFNG                 8         11         13         28         79         64
## IL22                 0          0          0          1          0          1
## LYZ              45380      49267      41434      29234      35023     100686
## CAPS2                1          1          5          6          2          3
## SYT1                 6          2          1         11          5          4
## BTG1              7750      11142       8477       7188       8179      10824
## HCAR3             3500       3052       3959       1730       4007       2206
## GJB2                 0          2          0          1          1          3
## GJB6                 5         62         17         40         15         15
## TNFSF11              0          0          3          2          5          0
## TPT1             55889      26642      62528      37984      48186      53195
## LMO7                55         11         93         58         39         63
## TNFSF13B          2067       3783       4179       2551       2456       2869
## LAMP1             3121       2490       2475       2148       2935       2845
## PSME2             1589       1192       1829        890        932       1806
## GZMB              1852        267        487        608        640       1075
## RPL36AL           2254       1594       1944       1689       1773       1909
## PYGL              5457      11141       3328       2985       5063       4885
## HIF1A             1670       3970       2255       2347       2253       2513
## FOS               3307      98136      19325      35592      65737      44138
## JDP2               730       1436        485        607        674        918
## NOXRED1              3         10          7          2         10          9
## SERPINA1         19419      35587      30512      16440      22309      23571
## CDC42BPB           184         59        288        146        283        218
## PLA2G4D              0          0          0          0          0          0
## TRIM69              18         13         26         18         11         21
## SLC51B               0          0          0          0          0          0
## SMAD3              571        178        662        443        491        503
## CYP1A1               0          0          1          0          2          1
## AKAP13            4337       5695       4727       3180       3949       5232
## MEFV              3887       3105       3142       1558       2631       3432
## SOCS1               33         93         94         42        128        126
## ATXN2L            1563        633       2027       1419       1503       1696
## CD19                93         61        110        127         92         56
## ITGAL             5975       2897       5282       3875       4614       6289
## ITGAM             5067       7574       3924       4606       5349       5309
## ITGAX             3706       5996       3321       4446       4165       4809
## DNAJA2             791        583        577        420        555        622
## SIAH1              112         87        103        105         84        121
## ADCY7             2881       1376       2820       2176       2351       2859
## NOD2               409       1171       1197        429        433        917
## CMTM2             2326       4413       1526       2055       2831       2325
## SF3B3              911        208       1011        798        701        861
## PSMD7              764        479        613        508        621        645
## WWOX                37         19         42         31         43         54
## MAF                597        192        580        303        406        423
## SLC7A5             206        267        320        153        171        233
## CXCL16            1551       4347       1436       2073       2096       1918
## XAF1               831       1396       3164        908        543       2532
## CD68              4813       2153       4731       1822       3772       4023
## PER1               177       2306        577        608        598        787
## NOS2                 0          0          3          0          2          0
## TRAF4               84         28         90         85         63         71
## CCL2                20          1          6          7         22         16
## CCL5              6484       1252       2471       1752       2309       4821
## CCL3                81         76        190        296        469        278
## CCR7               678         79       1108        560        426        906
## STAT3             6208       6090       5113       2825       4609       5020
## SOST                 0          0          0          0          0          0
## ITGA2B            2146        275        543        127        452       1627
## EFCAB13             10          6         22         18         14         12
## NPEPPS            1038        717        725        675        861        832
## TBX21              570         64        171        189        319        429
## COL1A1               0          0          0          1          0          0
## MRPS23             238         59        163         87        114        174
## MIR21                7          9          1          5          7          6
## RPS6KB1            348        230        372        245        306        371
## ACE                 14          7         81         26         48         29
## ERN1               839        978        749       1325       1042       1253
## PRTN3               21          9         14        223         66         11
## PLIN5               87        151         96        102        112        114
## RETN                88         56         57        238         70         42
## CCL25                0          0          0          0          1          0
## ICAM1             1146       2420       1936       1529       1694       1207
## TYK2              1966       1190       1365       1336       1575       1481
## SMARCA4            694        243        728        422        624        669
## ACP5               318        234        329        220        173        192
## JUNB             10319      43313      24353      16441      36807      34451
## CYP4F22             68          6         60          4         27         38
## JAK3              1164       1838       1974       2010       1487       1331
## JUND              3150       5046       5770       7879      12970       8906
## CEBPA              970        656        703        460        849        971
## CEBPG              298        132        304        237        249        281
## ACP7                 1          0          0          0          0          4
## ZFP36             6117      28576      17879      18584      33540      28502
## TGFB1             6631       4314       5003       2492       4538       5895
## RPS19            10293       3160      12141       7383       8492       9782
## PSG2                 0          0          0          0          0          0
## FUT2                 3          1          1          3          1          2
## NKG7              7340       1129       1963       2506       2738       6180
## ZNF415              11          7          3         16          5          3
## LILRB2            3522       3487       3603       2778       5565       4420
## LILRA5            3194       3124       1519       2331       4482       2319
## KIR3DL1            252         22         16         56        161         29
## KIR3DL2            149         41         73          7         53         78
## SMOX               302         92        127         45         79        200
## BMP2                 6          5          1          8         20          5
## GINS1               23          6         13          3          4          8
## PLCG1              588        140        976        598        465        735
## YWHAB             6734       6084       5066       3600       5301       5675
## PI3                395       1066        653        876       1673        644
## MMP9              1483      10778        866       1796       2012       2598
## CD40               141         38        275        129        105        105
## PFDN4               62         19         43         44         45         34
## BMP7                 0          0          0          0          0          0
## RPS21             4532       1572       5290       3422       3599       3867
## MX1               2114       1698       6528       2114        987       4989
## PFKL              1299        518       1264        682        987       1181
## IL17RA            6816       7696       4726       4385       5704       5912
## UBE2L3            1415        790        970        628        913       1030
## TPST2             1523        561       1130        795       1280       1619
## XBP1              1691        675        977        720        750       1009
## UQCR10             757        343        555        375        519        542
## SEC14L2             19          6         62         27         16         50
## APOL6             2253       2366       3709       1207       1016       2812
## APOL1              856        904       1235        395        532        807
## TYMP              4615       4130       5303       2166       3580       5974
## BEND2               73         52         51         15         51        124
## PHEX                15          6         21          6         11          8
## TIMP1             1790       1028       1239       1716       1965       1530
## FOXP3               59         10         90         59         67         45
## MSN              29272      23663      20212      17746      24291      27058
## PGK1              6556       9018       7202       6292       8259       8013
## LAMP2             7968      10084       6093       5033       7004       6600
## CD40LG             144         22        164         86        121        118
## IRAK1             1466        929       1487       1121       1451       1768
## COX2             42577      30923      51614      38148      39017      53421
##             GSM3308479 GSM3308480 GSM3308481 GSM3308482 GSM3308483 GSM3308484
## TNFRSF9             76        141         96         67         54        165
## ENO1              4239       5417       7166       7280       6460       7493
## PIK3CD            7748       6449       6347       4935       4400       7453
## PGD               6270       7853       6213       5045       3256       7933
## MTHFR              310        329        490        412        429        251
## TNFRSF1B         13659      15086      14604      17217      10640      15233
## PINK1             1000       1102        805        646        593       1175
## IFNLR1               7         23         60         73         63         51
## RUNX3             1578       2660       2063       7677       7023       2202
## SH3BGRL3         10057      10035      10234      13008      10675      11299
## CD52              1524        870       4024       4607       5817       4205
## IFI6               528      13513       1025       3411       1800        644
## ZC3H12A            602        394        189        536        310        440
## UTP11               73         54        128         90        119         93
## JUN               8098       5534        839       5141       1617        434
## KANK4                0          0          0          0          0          0
## EFCAB7              17         18         39         18         39         23
## IL23R                1          0          3          1          4          6
## ADGRL2               1          0          0          0          0          0
## GBP3                87        167        625        200        276        188
## GBP1               515       1878       3435       1331        887        602
## GBP5              1317       2840       7826       3589       2108       1433
## TGFBR3             351        295        355       1702       2164        342
## VCAM1                1          0          2          8          1          1
## PTPN22             211        236        529        387        571        349
## CD160              143         92         29        253        252         58
## FCGR1A             449        677       1782       1165        482       1393
## MCL1             44213      37895      20011      17398      16557      17498
## CTSK                23         54         36         43         45         25
## RORC                16          2        102         65         76         72
## S100A9          180814     195635     119661      93553      61372     219679
## S100A12           4730       7305       5628       2351       1527       8556
## S100A8           66810      83323      46202      34890      22805      86146
## IL6R              5092       4826       6486       4136       3175       6409
## RIT1              2212       1270       1211       1109        949       1660
## BGLAP                6          3          4          6          9          7
## IFI16             3679       5162       4415       3045       2750       4275
## AIM2               204        279        391        143         89        259
## CRP                  0          0          0          0          0          0
## FCGR2A           15552      11228      11047      11536       5991      17880
## HSPA6             2287       1797       1660       1499       1025       1930
## FCGR3A           23106      22896      19352      20338      14284      17463
## SELL             59941      68748      52779      33463      28916      47567
## GLUL             22047      14484       9643      12521       8588      15721
## PTGS2            16894      11861      10153       2379       1204       3358
## CRB1                 1          1          2          2          1          1
## KDM5B              667        540        385        352        326        426
## IL10                 7          8          1          5          4          0
## YOD1               445        269        164        242        223        194
## HHAT                 9         22         29         45         46         37
## TRAF5               94        102        241        251        491        266
## NLRP3              746        847        898        911        644        531
## LINC01250            0          0          0          0          0          1
## RPS7              4187       3787       8325       7762      13122       9828
## RSAD2              155       9417        535       1548        838        135
## FOSL2             4378       3834       2720       4308       3685       3549
## REL                874        730       1043       1229       1059        905
## TGFA               844        493        456        329        296        632
## DYSF              8075       9367       6383       4066       2406       8761
## HK2               1486       2235       1822        831        647       1362
## CD8A               429        409       1314       4023       1900       1263
## CD8B               113        109        592       1248        874       1088
## EIF5B              204        177        699        450        770        516
## IL1R1              713        416        160        187        119        239
## RGPD6               41         31         90         56         98         71
## IL1A                 3          0          0          0          0          0
## IL1B              1915        183        506        360        181        548
## IL37                 0          0          0          1          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             3478       3802       1863       2581       1359       3253
## NMI               2040       1859       1796       1359       1349       1880
## TNFAIP6           1240        797        245        388        169        440
## IFIH1              226       1107        509        487        378        292
## SCN1A                0          0          0          0          0          0
## ABCB11               1          1          0          1          0          0
## RBM45               22         23         75         44         78         44
## FRZB                 0          0          0          0          0          1
## TFPI                 4          1          2          3          3          6
## STAT1             3908       6206       9625       5055       3852       3163
## NABP1             1112        744        543        374        265        497
## SF3B1             3995       3245       3872       3964       4719       4282
## CASP10             283        433        432        369        387        275
## CD28               126         73        730        525        824        512
## CTLA4               24         27         32         96        105         72
## ICOS                28         19        207        164        327        166
## NDUFS1             425        407        656        554        632        539
## CXCR2            27230      15511      15104      14900       8604      22579
## IRS1                24         28         88         52         96         81
## CCL20               45          0          0          1          0          0
## ATG16L1            221        186        285        302        402        239
## GPR35               48        109         87        147        139        118
## PDCD1               10         25         36         58         59         27
## PPARG               11          5          3          9          3          2
## RPL15             6303       5848      14793      14626      20996      15657
## EOMES               57         85        104        241        257         66
## CX3CR1             704        900       2352       2069       1357        963
## ACKR2                0          1          1          3          2          0
## CCR2               484        628       2437        868        443        950
## CCRL2               27         29         46         44         38         24
## TLR9                62         65         63         54         44         81
## ARHGEF3            588        848       1151       1340       1628        742
## ADAMTS9              0          0          0          0          0          0
## TMEM45A             21          4          4          4          3          8
## CD80                 0          2          6          6          7          1
## CD86               439        720       1691       1143        833        674
## MIX23               14          5         42         19         36         21
## PLS1                 6          4         24         24         30         15
## PTX3                88         57         47         52         48         48
## GOLIM4              57         49        158        102         83         78
## MYNN               322        207        315        330        355        328
## TNFSF10           3391       5631       5436       2439       1843       3556
## ADIPOQ               0          0          0          0          0          0
## SPON2              740       1659        102       1494       1534        135
## S100P             9018       3021       1779       1726       2327       2615
## WDR1              6544       6278       6424       6337       5518       6097
## CD38               131        262        258        375        346        271
## PPARGC1A             2          0         20          0          6          9
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          0          0          0          0
## CXCL8           141249      17292      11250      15401       4842      11886
## CXCL2               77          8          7          2          1          2
## AREG               328        386          2         97         79          1
## CXCL10              14         29         51         28         27         16
## CXCL13               0          0          1          1          1          0
## SPP1               194         30         77         26         79         50
## HERC6               90        688        194        257        335        162
## NFKB1              598        560       1314        802        924       1228
## SEC24B             495        343        485        407        450        371
## EGF                 43         22         23         21         21         26
## IL2                  1          1          1          0          0          0
## IL21                 0          1          3          0          0          2
## IL21-AS1             0          1          3          0          0          5
## SLC7A11             42          4         20         17          3         31
## IL15                55         84        190         95         90         64
## EDNRA                0          0          0          0          0          0
## TLR2             15386       7839       3409       3548       2081       4873
## FGB                  0          0          0          0          0          0
## DDX60              195       1884        582        667        557        243
## SPCS3             1761        925       2532       1817       2475       2196
## TLR3                 2          1         29         11         25          5
## OSMR                32         22         28         36         23         21
## GZMK               120        125        641        968       1272        659
## GZMA               580        630        756       2091       2481        653
## ANKRD55             73         77         74         53        136         74
## CENPK               22          6        112         42        131         99
## CAST              1827       2001       3885       3621       3899       3138
## ERAP1              741        832       2004       1386       1753       1729
## ERAP2             1633        153        185       3760       2214       1287
## TNFAIP8            888        548       1716       1266       1977       1475
## CSF2                 0          0          0          0          0          0
## IL5                  0          0          1          0          1          0
## IL13                 0          0          0          1          0          0
## IL4                  1          2          2          1          2          3
## CD14              3421       5263       7872       8986       6119      10663
## CSNK1A1           1505       1336       2168       1435       1641       1680
## PPARGC1B           110        213        132        108        118         85
## TNIP1             4975       4751       4151       4353       3389       6493
## ATOX1              156        202        209        185        183        170
## FAXDC2             101        115        188        124        156        161
## IL12B                4          2          0          1          1          1
## MIR146A              0          0          0          0          0          0
## PDLIM7            2588       2279       1172       1414        804       1710
## SERPINB1          5683       6053       3991       4603       3466       6193
## SSR1              1786       1313       3144       2395       2713       2580
## CD83               240        248        347        556        683        281
## SOX4               140        225        160        112         90        118
## CMAHP               34         40         56         62        122         59
## HLA-A            46475      50566      45181      46462      36938      41412
## HLA-C            99687     114247      62213     109946      63631      62308
## HLA-B           121993     135042     107404     103946      93755      72727
## MICA                76         95        228         92        128        113
## LTA                 25         15         82         45         77         70
## TNF                187         64        237        326        117        235
## HLA-DRB1          2806       3641       5789       5492       3592       1616
## HLA-DQB1          1724        797        614       2708        395        199
## PPARD              170        134        322        383        372        296
## CCND3            10333       9775       3672       4897       5660       4008
## VEGFA              168        175        155        223         73        113
## RUNX2              567        338        343        333        572        375
## IL17A                0          0          0          0          0          0
## IL17F                0          0          0          0          0          0
## PRDM1             1024        619        618        891       1029        312
## ATG5               304        236        482        377        532        359
## TRAF3IP2            91        156        166        157        268        207
## NCOA7              246        283        604        434        611        358
## SGK1              1842       1280       3520       2466       1827       3239
## IFNGR1            7484       3171       3176       2326       2015       4131
## TNFAIP3          16597       5208       1076       4672       5676       1445
## SOD2             42566      24016      35092      36778      25446      58887
## LPAL2               13          9          5         14         25          7
## PLG                  0          1          0          0          1          0
## CCR6                20         10        183        102        118         90
## RAC1              2853       2539       3043       2609       2500       2890
## ZNF316             688        775        449        732        537        666
## AHR                791        744       1187       1197       1044        656
## IL6                  0          1          1          1          9          2
## TOMM7             1057       1042       2065       2055       3559       1996
## CYCS               341        280        650        522        755        519
## AQP1                 6          5          5          2          3          4
## NT5C3A             813       1083        776        657        737        728
## EGFR                 0          1          0          0          0          0
## CD36              1159       1679       4106       2086       1523       2597
## SAMD9             1603       3799       2096       2017       1450       1643
## SERPINE1             8          3         14          8          8          3
## CUX1              1591       2001       1779       1797       1372       1640
## PSMC2              157        286        537        400        517        333
## NAMPT            88473      40641      34419      34555      30871      78661
## HYAL4                0          0          0          0          0          0
## LEP                  4          1          3          2          0          4
## CALD1               11          9         12          6         12         16
## BRAF               795        727        663        594        601        683
## EZH2                34         40         44         42         91         72
## DNAJB6            1694       1337       1351       1569       1306       1718
## CSMD1                7          1          0         32          0          0
## CTSB              5371       6957       9075       5977       5427       5628
## EGR3               680        373        407        885        449       1046
## TNFRSF10A           51         55        204        139        185        146
## BNIP3L            2918       2111       2217       1736       1790       2631
## DUSP4                9         20         30         83         93         12
## NRG1                19         31        172        270         82        115
## RPL7              4395       3271       9731       8948      14529      10305
## IL7                  1          6         18         12         14         12
## GEM                  0          0          1          0          1          1
## MYC                196        141        897        837       1259        847
## GPT                  1          0          3          2          5          0
## JAK2              1294       1476       1881        909        870       1115
## CD274               98        128        254        269         88        140
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              2          2          0          2          2          2
## TTC39B              79         47        165        122        238        121
## IFNA1                0          0          0          0          0          0
## TEK                 14         29          4         11          1         13
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              109        120        286        253        325        216
## ANXA1             4865       8301       8502      10038       7984       6104
## ERP44             1252       1579       1497       1332       1160       1336
## ZNF483              12          6         23         29         30         15
## TNFSF15              2         13          6          4          1          7
## TLR4             10484      10469       7541       5027       3732      11464
## PTGS1              541        638        726        582        485        879
## HSPA5             5893       4080       3925       5313       5362       5102
## FNBP1             3136       3112       4009       3823       4451       3414
## CARD9              132        201        253        163        103        122
## TRAF2               63         62        148        128        136        104
## CLIC3              141        242         45        307        185         30
## IL2RA               49         40        123         89        188         76
## GATA3               88         89        435        358        492        217
## VIM              16412      17053      19366      21548      14994      15331
## CREM               156         90        126        224        254        155
## DKK1                 0          0          0          0          0          1
## MBL2                 0          0          0          0          0          0
## SAR1A              719        546        908        750        790        828
## PRF1              1796       3099       1234       7022       4840       1028
## ZMIZ1             2048       1907       1820       2407       1708       1570
## IFIT3             3365      35361       4510       6451       3393       1942
## TALDO1           12923       9946       8879       8401       5396      12138
## IGF2                 1          0          0          1          0          0
## INS-IGF2             1          0          0          1          0          0
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1              980       1257       1545       1547       1649       1196
## TRIM22            3407       8639       4264       2780       2761       2003
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          0          0          0          0
## SLC1A2               0          1          1          2          0          0
## FOSL1               31         48         14        107         48         36
## CCND1                0          3          3         10         10          5
## JRKL                44         44        113         60        103         76
## MMP7                 0          0          0          0          1          0
## MMP1                 0          2          1          0          0          0
## MMP3                 0          0          0          0          0          0
## CASP1             2949       4349       4242       3269       2311       3224
## DLAT                83         91        256        194        295        189
## IL18               131         87        137         88         65         67
## CD3E               908        583       3022       3420       6781       3028
## MCAM               275        209        245        194        227        304
## WNK1              3470       2952       4211       3785       3520       3602
## TNFRSF1A          4526       3507       4349       3187       2001       5191
## GAPDH            17522      16269      18227      21902      16022      23142
## CD4               1466       2207       5562       4465       5175       3093
## SLC2A3           10293      11010       6890       8050       6460      12909
## CLEC4D            1220       1814        559        217        209        868
## KLRB1              556        421        503       1119       1573        943
## CD69              1663        798        307       1134       2035        584
## CLEC2B            1621        918       1311       1391       1366       2124
## OLR1                64         53          5         15         13         56
## ABCD2               43         21        228        160        276        171
## LRRK2            19093      12876       9806       6842       3378       7781
## VDR                434        433        518        455        175        564
## TMBIM6           15329      12289      15005      13918      13063      16753
## PFDN5             1941       1887       3580       3549       4531       3907
## SP7                  0          0          0          0          0          0
## MUCL1                0          0          0          0          0          0
## CD63              3648       3521       2567       3103       2318       3515
## SUOX              1276        971       1111       1042        874       1156
## RPS26             2594        490       3303        864       5713       3769
## RPL41             3794       4045       7688       7636      11972       8130
## IL23A                7         20         42         34         48         35
## DDIT3              888        622        190        319        323        459
## IFNG                29         28          7         17         16          4
## IL22                 0          0          0          0          1          0
## LYZ              88414      86221     120660      51424      39935      77249
## CAPS2                5          2          2          7          4          1
## SYT1                 1          0          6          3          1          5
## BTG1             13415       8912       7388       9368       8774       7835
## HCAR3             3210       1679       1938       2135       1015       5681
## GJB2                 1          1          1          1          0          1
## GJB6                14         27          4          9          8         18
## TNFSF11              1          2          1          9          5          3
## TPT1             33863      25691      58601      47915      84417      69274
## LMO7                32         10         80         50        124         80
## TNFSF13B          1998       2554       2713       2296       1632       2582
## LAMP1             2643       2556       2860       3019       2733       3154
## PSME2              810       1549       2344       1847       1743        989
## GZMB               502       1031        489       1933       2073        246
## RPL36AL           1407       1445       2218       1855       3292       2567
## PYGL              9621       7326       5558       3651       2531      10609
## HIF1A             2300       2214       1721       2068       1596       1956
## FOS              68457      73043      14299      19092       4655       9169
## JDP2              2074       2549        658        754        489        833
## NOXRED1             15          6          4          7          1          9
## SERPINA1         30893      25712      19541      21968      11291      27733
## CDC42BPB           157        223        352        209        225        186
## PLA2G4D              0          0          0          0          0          0
## TRIM69               7          9         19         16         15         17
## SLC51B               0          0          0          0          0          0
## SMAD3              200        301        657        875        949        505
## CYP1A1               0          0          0          1          0          3
## AKAP13            6400       6619       5618       5433       5040       4083
## MEFV              3397       3751       3362       2753       1421       2790
## SOCS1              153        207         47        112         67         31
## ATXN2L            1011       1226       1724       1798       2265       1643
## CD19                 0         28         86        112        144        123
## ITGAL             4467       6187       5938       6858       7258       4374
## ITGAM             7037       7165       5991       5175       4034       7118
## ITGAX             7376       6287       3593       3748       2432       4603
## DNAJA2             711        646        878        503        683        805
## SIAH1              139        105        118        112        110        104
## ADCY7             2268       3234       3548       3371       2840       2239
## NOD2               796        505        768        794        426        967
## CMTM2             4903       2807       2323       1676       1327       3226
## SF3B3              391        539       1119        939       1243        805
## PSMD7              616        554        737        706        802        772
## WWOX                19         25         37         66         84         42
## MAF                120        207        519        701        608        291
## SLC7A5             222        133        179        302        380        251
## CXCL16            4630       2283       1720       2349       1576       1942
## XAF1               278       3640       1073       1254       1224        515
## CD68              2685       4076       6464       6077       3519       2898
## PER1              4536       3447        285        815        840        255
## NOS2                 1          0          0          5          2          4
## TRAF4               18         36         58        101        143         61
## CCL2                 0          3         38         33         27         10
## CCL5              1507       2172       2122       7491       9407       2270
## CCL3               980        300         90         99         53         32
## CCR7               202         85       1036        751       1221       1015
## STAT3             6857       5681       5382       4242       3455       5629
## SOST                 0          0          0          0          0          0
## ITGA2B             346        424        322        246        191        509
## EFCAB13             11          8         22         32         34         19
## NPEPPS            1162       1011       1005        649        648       1083
## TBX21              265        386        139        760        869        136
## COL1A1               1          3          0          0          0          0
## MRPS23              88         83        273        165        231        182
## MIR21                8         11          4          6          2          7
## RPS6KB1            335        209        483        442        482        383
## ACE                  4          5         78         38         64         26
## ERN1              2782       1062       1057        824       1697        975
## PRTN3              116         80          1         14          8         20
## PLIN5              169        187         76         54         49        102
## RETN               144        217         61         71         26        114
## CCL25                1          2          0          2          0          1
## ICAM1             1369        933       1334       1797       1164       1979
## TYK2              2124       2227       2002       1546       1346       1508
## SMARCA4            404        494        720        757        970        571
## ACP5               122        113        421        399        357        249
## JUNB             70681      30392      13303      24046      14982      15835
## CYP4F22             38         76         77         70         29          7
## JAK3              1468       1549        951       1257       1520       1792
## JUND              9421      11950       3254       7009       5254       3179
## CEBPA              666       1217       1222        831        576        934
## CEBPG              166        174        402        285        346        250
## ACP7                 0          0          1          0          0          0
## ZFP36            74369      22579       8994      13532       7822       8026
## TGFB1             4607       6252       4611       5997       5667       4647
## RPS19             3909       4295       9712      10982      15308      10514
## PSG2                 0          0          0          0          0          0
## FUT2                 1          1          2          2          1          1
## NKG7              2510       3735       1254       8104       8982       1723
## ZNF415               1         13          8         26          2          6
## LILRB2            4806       5394       4486       5414       3218       4066
## LILRA5            2201       3560       2873       2932       2232       4543
## KIR3DL1             83        102         11         79        235         34
## KIR3DL2             36         35         12         34        100         19
## SMOX                81         54         73         84         76        141
## BMP2                20          7         10          2          1         13
## GINS1                5          8         11          7         13          9
## PLCG1              242        213        772        631       1268        786
## YWHAB             5288       5609       6709       5743       5854       6074
## PI3                652        291        686       1214        267       1624
## MMP9              7669      10488       3643        798        881       4171
## CD40                29         41        368        172        225        166
## PFDN4               22         16         59         45         44         45
## BMP7                 0          0          0          0          0          0
## RPS21             1981       1683       4478       4620       7817       5268
## MX1                708       9716       1534       2241       1365        747
## PFKL               600       1079       1504       1390       1434        981
## IL17RA            8409       9432       7470       4696       3724       7315
## UBE2L3             818        918       1320       1123       1261       1185
## TPST2             1244        984       1020       1740       1556       1542
## XBP1               570        571       1267       1164       1892       1363
## UQCR10             413        458        643        635        672        587
## SEC14L2             11          2         19         25         45         30
## APOL6              954       2302       3193       2201       1373        955
## APOL1              443        863       1069        910        506        513
## TYMP              4112       8514       4399       4578       2917       2766
## BEND2               51         40         46         37         46         66
## PHEX                 4          2          9         16          8         12
## TIMP1             2415        913       1633       2149       1628       2047
## FOXP3               21         26         81         71        128         64
## MSN              28453      26670      22267      25192      22331      26756
## PGK1              9045       7220       8274       7712       7290      10467
## LAMP2            10173       6322       6113       5420       4492       8174
## CD40LG              46         25        299        131        304        150
## IRAK1             1402       1367       1379       1642       1563       1159
## COX2             28929      32135      48513      45066      75172      50998
##             GSM3308485 GSM3308486 GSM3308487 GSM3308488 GSM3308489 GSM3308490
## TNFRSF9             65        148        102        125         76        101
## ENO1              5887       7041       7128       7442       7057       6942
## PIK3CD            3682       5947       6731       7862       6434       6526
## PGD               3094       5208       6307       6748       3930       6563
## MTHFR              287        355        357        520        588        283
## TNFRSF1B          9568      14651      13382      13161      11511      16570
## PINK1              419       1001        975        927        651        943
## IFNLR1              58         37         74         76         74         25
## RUNX3             3007       3426       3642       2825       3007       2079
## SH3BGRL3          7503      10229      12007      10685       8874      10941
## CD52              3581       4328       4049       5967       5283       4267
## IFI6               775        785       1763        931        601       3242
## ZC3H12A            269        458        346        231        251        280
## UTP11               87         58         65        172        149         82
## JUN               2942       2647       4654        423        262      15498
## KANK4                0          0          0          0          0          0
## EFCAB7              17         26         26         28         36         21
## IL23R                4          7          1          2          2          6
## ADGRL2               0          0          2          0          0          0
## GBP3               145        142        185         48        257        265
## GBP1               357        305       1756       1205       1452       1146
## GBP5              1049        919       3888       2309       4222       2272
## TGFBR3             745        574       1015        416        627        295
## VCAM1                1          3          0          3          4          0
## PTPN22             306        335        326        478        586        278
## CD160              117         55         57        102        101         54
## FCGR1A             404        549       1972        566        824        618
## MCL1             10759      21457      22508      21067      18814      37507
## CTSK                28         34         21         28         46         43
## RORC                81         50         30        142        292         93
## S100A9           70185     116062     139233      99934      59565     165127
## S100A12           2757       5398       3782       3491       1653       5023
## S100A8           25996      45142      52973      34443      23975      61638
## IL6R              2736       3745       5548       5901       5050       4283
## RIT1               834       1508       1289       1269        935       1583
## BGLAP                4          8          8         12          4          8
## IFI16             1506       2366       3930       3805       3628       3380
## AIM2                74        121        142        115        199        201
## CRP                  0          0          0          0          0          0
## FCGR2A            5756      12250      15841      15563      10396      12725
## HSPA6              715       1677       1836       2327       2084       1966
## FCGR3A            7690      13576      19482      18513      15076      12386
## SELL             19602      24473      36293      31577      23058      55215
## GLUL              8182      16836      14654      11588       8989      13120
## PTGS2              872       3025       5826      11417       7152       9915
## CRB1                 1          1          1          2          2          1
## KDM5B              258        470        319        577        529        488
## IL10                 5          2          1          1          2         23
## YOD1               182        232        125        117        189        277
## HHAT                36         39         30         30         39         31
## TRAF5              280        270        195        427        505        230
## NLRP3              483        741       1010        805        495       1105
## LINC01250            0          0          0          2          0          0
## RPS7              9106      10264       7814       9777      10012       7499
## RSAD2              172        235        824        372        334       2798
## FOSL2             2094       3498       3033       2758       2211       3196
## REL                870       1053        789       1344       1250        971
## TGFA               330        536        493        570        425        671
## DYSF              2411       5687       5956       4871       3530       6398
## HK2                455       1100        664       1785        846       1826
## CD8A              1173       1603       2790        864       1536        598
## CD8B               629       1079        874        427        757        360
## EIF5B              399        427        424        678        812        494
## IL1R1              168        381        210        151        178        319
## RGPD6               67         66         45         82        125         48
## IL1A                 1          0          0          0          0          1
## IL1B               131        256        654       1566        877        324
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             1416       2450       3335       2092       1457       2024
## NMI                983       1155       1844       1325       1233       2152
## TNFAIP6            217        353        624        333        191        878
## IFIH1              191        258        394        438        519        575
## SCN1A                0          0          0          0          0          0
## ABCB11               1          1          2          0          1          0
## RBM45               47         44         38         67         72         58
## FRZB                 0          0          0          2          0          0
## TFPI                 3          3          5         13          9          2
## STAT1             2262       2775       6089       5592       4613       3716
## NABP1              233        380        444        430        479        756
## SF3B1             2974       4255       4102       3939       4376       4244
## CASP10             226        270        331        444        477        378
## CD28               621        663        257        614       1083        589
## CTLA4               46         54         17         41         63         60
## ICOS               150        186         80        146        258        103
## NDUFS1             367        489        492        746        608        493
## CXCR2             8019      21603      24490      29096      19924      25966
## IRS1                78        143         81        107         92         60
## CCL20                1          0          0          1          4          2
## ATG16L1            231        215        179        280        306        211
## GPR35              101         70        116         58         87         92
## PDCD1               36         26         20         68         71         52
## PPARG                4          4          8          5          8          7
## RPL15            14362      17061      12934      17263      17507      11741
## EOMES              111        117        119        201        248         65
## CX3CR1             576        397       1556       2350       2099       1002
## ACKR2                1          0          0          3          0          0
## CCR2               778        754        823       1592       1805       1763
## CCRL2               24         21         42         46         32         49
## TLR9                46         81         80        132        132         62
## ARHGEF3            819        750        821       1021       1302        741
## ADAMTS9              0          0          0          0          0          0
## TMEM45A              3          0          3          3          2          2
## CD80                 7          7          4          8          9          7
## CD86               795       1018       1079       1010        940       1104
## MIX23               19         23         38         36         50         12
## PLS1                15         42         29         14         19         21
## PTX3                47         52         82         30         32         27
## GOLIM4              87         56         73        136        144         84
## MYNN               193        259        301        330        328        268
## TNFSF10           1217       1869       4331       3823       3569       4584
## ADIPOQ               0          0          0          0          0          0
## SPON2              250         86        329        600        182        327
## S100P             2244       3581       4724       2811        149       2303
## WDR1              4135       5468       6449       6970       6606       5877
## CD38               173        109        157        395        165        168
## PPARGC1A             2         16          2          5          5          5
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          2          0          0          0          0
## CXCL8            11559      26568      24013      10986       3621      35418
## CXCL2                1          8         13          2          4         14
## AREG                35         39         30          6          3        224
## CXCL10              21         13         45         42         24         11
## CXCL13               0          0          0          1          0          0
## SPP1                52         18        195        150         24         33
## HERC6              143        139        170        220        239        259
## NFKB1              686        959        774       1451       1423        945
## SEC24B             322        490        392        567        630        464
## EGF                 23         24         41         47         52         18
## IL2                  1          1          1          1          2          0
## IL21                 0          0          1          2          0          4
## IL21-AS1             0          0          5          0          1          1
## SLC7A11             12         12         16         13         13         14
## IL15                41         54         79         86         90         74
## EDNRA                0          0          0          0          0          0
## TLR2              2264       4074       5399       3937       3624       7317
## FGB                  0          0          0          0          0          0
## DDX60              227        203        350        430        507        829
## SPCS3             1748       1800       1898       2520       2519       2030
## TLR3                 8          7          9         18         21          2
## OSMR                17         32         21         19         18         34
## GZMK              1192        656        221        367        872        464
## GZMA              1211        854       1542        825        966        624
## ANKRD55             34        158         25         66        111        101
## CENPK               73         66         37         48         88         77
## CAST              2538       2413       2949       3055       2797       2592
## ERAP1             1627       1169       1274       2176       2563       1157
## ERAP2             1394       1538       2880       1637       1998        170
## TNFAIP8           1287       1519        995       1962       2296       1233
## CSF2                 0          0          0          1          2          0
## IL5                  1          0          0          0          1          0
## IL13                 0          0          0          0          0          0
## IL4                  3          4          2         10          4          0
## CD14              8037      12600       9188       7750       5544      10297
## CSNK1A1           1048       1473       1356       2549       2507       1834
## PPARGC1B            79         92         83         67        103        119
## TNIP1             2932       4380       3945       4082       3548       5836
## ATOX1              123        159        220        217        147        228
## FAXDC2             113        180        162        260        265        108
## IL12B                1          1          2          0          1          1
## MIR146A              0          0          0          0          0          0
## PDLIM7             866       1713       1732       1433        889       2125
## SERPINB1          2875       4220       5951       5173       3782       5361
## SSR1              1926       2436       2321       2588       2678       2571
## CD83               408        314        591        255        160        144
## SOX4               177        133        133        170        144        217
## CMAHP               71         63         80         80         85        101
## HLA-A            32322      43467      61777      46083      39190      51486
## HLA-C            40753      46205      98016      80980      53425     118637
## HLA-B            55318     106560     113999     103173      85372     103510
## MICA                94        100        135        127        123        131
## LTA                 57         56         60        119        100         65
## TNF                179        154        233        162        199         21
## HLA-DRB1          3120       6037       4973       5564       3131       3743
## HLA-DQB1           566       1473       4485       1607        488        238
## PPARD              252        405        221        407        479        283
## CCND3             3364       5290       4733       4578       5368       6124
## VEGFA              126        157        155        112        125        250
## RUNX2              454        772        332        452        425        496
## IL17A                0          0          0          0          0          0
## IL17F                0          0          0          2          0          0
## PRDM1              441        593        673        767        887       1203
## ATG5               349        380        359        445        508        347
## TRAF3IP2           169        277        165        207        274        196
## NCOA7              353        296        381        475        544        377
## SGK1              1421       2326       2777       4163       2959       1497
## IFNGR1            1803       2971       3243       4128       3441       4741
## TNFAIP3           3048       3343       2126        820       1067       7119
## SOD2             21349      37490      48427      45203      28540      29308
## LPAL2                8         10          9         10         15          6
## PLG                  0          0          0          0          0          0
## CCR6               134         91         64        463        436         72
## RAC1              1942       3190       3858       3750       2926       2711
## ZNF316             477        676        729        551        513        791
## AHR                981        770        845        682        629        889
## IL6                  5          4          1          5          6          3
## TOMM7             2124       3212       1834       2459       2946       1848
## CYCS               538        417        525        628        690        609
## AQP1                 0          4          6          1          0          0
## NT5C3A             430        691        871        768        710        854
## EGFR                 0          0          0          0          0          0
## CD36              2124       1702       3819       2281       1875       3548
## SAMD9              944       1163       1906       1779       1791       2919
## SERPINE1             6          6          8         17         24          3
## CUX1              1138       1632       1550       1297       1432       1632
## PSMC2              282        289        349        587        558        337
## NAMPT            26973      55338      48800      38327      29914      54807
## HYAL4                1          0          0          0          0          0
## LEP                  2          1          1          5          5          3
## CALD1               14          8         24         16         35          4
## BRAF               468        760        564        674        704        780
## EZH2                43         46         49         57         74         53
## DNAJB6             953       1426       1635       1544       1436       1442
## CSMD1                0          2          0          2          5          0
## CTSB              5502       5470       8118       6760       6432       7557
## EGR3               263        261        974        395        166        268
## TNFRSF10A          143        140         99        159        219        124
## BNIP3L            1443       2070       2171       2572       2092       2252
## DUSP4               35         56         20         21         36         54
## NRG1                96        204        121         35         52        399
## RPL7             10430      13251       8235      10944      13134       8300
## IL7                 22         12         26         42         38          7
## GEM                  0          0          1          2          4          0
## MYC                695       1332        697       1098       1511        984
## GPT                  1          0          2          2          0          1
## JAK2               582        757       1189       1134       1040       1245
## CD274               73        161        416        158        197         82
## IL33                 1          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              0          0          0          2          3          0
## TTC39B             136        150        130        133        203        138
## IFNA1                0          0          0          0          0          0
## TEK                  2         11         18         18         37          5
## TRBV20OR9-2          0          1          0          0          0          0
## TOMM5              246        196        222        275        272        196
## ANXA1             5461       5870      11230       6474       6473       6464
## ERP44              967       1254       1467       1292       1101       1555
## ZNF483              30         23          9         27         53         30
## TNFSF15              1          3          3          4          7          7
## TLR4              3140       6232       7182       5640       5244      12584
## PTGS1              610        603        881       1138        897        580
## HSPA5             4068       6020       5896       5129       4514       5567
## FNBP1             2997       3936       3435       4474       4551       3265
## CARD9              131        104        132        150        126        193
## TRAF2               90        110         98        167        180         96
## CLIC3               79         37         92        126         77        105
## IL2RA               92         94         61        152        213        169
## GATA3              271        259        207        420        589        243
## VIM              13448      22450      24980      16982      15521      21364
## CREM               129        148        109        130        101        186
## DKK1                 0          0          0          0          0          0
## MBL2                 0          0          0          0          1          0
## SAR1A              535        696        740        910        903        693
## PRF1              1394       1159       3219       2769       2179       1392
## ZMIZ1             1523       2446       2271       2441       1894       2509
## IFIT3             1436       1869       6619       2807       2833      11579
## TALDO1            5170       9801      10800      11678       6744       9385
## IGF2                 0          0          0          0          0          1
## INS-IGF2             0          0          0          0          0          1
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1              998       1531       1356       1669       1642       1324
## TRIM22            1413       1743       3502       3258       3907       4436
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          0          0          0          0
## SLC1A2               0          3          0          0          1          0
## FOSL1               14         38         49         11          5         19
## CCND1                6          6          6         10          4          6
## JRKL                63         62         57        132        162         88
## MMP7                 0          0          0          0          0          0
## MMP1                 0          2          8          0          6          0
## MMP3                 0          0          0          0          0          0
## CASP1             1779       2300       3452       2743       2429       2718
## DLAT               183        186        176        263        299        151
## IL18               100         95        152         85         92        122
## CD3E              3471       3989       2759       2563       4635       3129
## MCAM               170        248        214        211        283        206
## WNK1              2507       4730       3411       4896       5009       4940
## TNFRSF1A          1858       3566       5020       5579       3947       4121
## GAPDH            14132      18924      21154      18008      14885      20405
## CD4               3948       4800       3539       3724       4508       5116
## SLC2A3            4524      10173       9664       5503       4165       6624
## CLEC4D             220        473        565        295        299        608
## KLRB1             1292        735        554       1199       1114        688
## CD69               938        788        698        386        372       1847
## CLEC2B             939       1612       2020       1166       1289       1930
## OLR1                 4         14        154         22         53         14
## ABCD2              154        188        105        169        303        152
## LRRK2             4795       6463       7395       6768       6250       7279
## VDR                228        440        394        446        422        471
## TMBIM6            8699      13919      15304      15664      13709      14319
## PFDN5             3041       3811       3193       3485       3647       2960
## SP7                  0          0          0          0          0          0
## MUCL1                0          0          0          0          0          0
## CD63              1776       3391       3707       2806       2157       3478
## SUOX               714       1077       1152       1318       1098       1159
## RPS26             3587        743       3119        836       4380       2905
## RPL41             7670       9780       7037       8967       9148       7468
## IL23A               35         41         12         46         76         31
## DDIT3              239        458        423        249        219        278
## IFNG                 7          9         38          8         14          3
## IL22                 0          1          0          0          0          0
## LYZ              79371      97990     102698      68481      32333     117457
## CAPS2                4          4          4          8          4          4
## SYT1                 0          3          7          6          3          8
## BTG1              6114      10290       7997       8504       8283      14502
## HCAR3             1043       1842       4043       2205       1560       1350
## GJB2                 0          0          0          0          0          0
## GJB6                 4          9         11          4          6          5
## TNFSF11              2          2          1          2          8          1
## TPT1             59404      65625      49532      56599      65120      49163
## LMO7                47         84         47        101        154         64
## TNFSF13B          1373       1983       2561       2073       1679       3296
## LAMP1             2132       2880       3051       2730       2685       3157
## PSME2              982        857       1548       1385       1260       1138
## GZMB               398        593       1402        997        556        557
## RPL36AL           2167       2918       2097       2066       1959       2494
## PYGL              3023       5322       6486       5397       3252       4874
## HIF1A             1302       2488       1483       2455       1744       2466
## FOS              14735      24711      31575      16107      11384     105817
## JDP2               386        756        781        597        462       2003
## NOXRED1              7          8          1          4          5         13
## SERPINA1         15407      27008      24775      21378      13924      30699
## CDC42BPB           160        255        233        224        247        246
## PLA2G4D              0          0          0          0          0          0
## TRIM69               7         21         14         11         19         25
## SLC51B               0          0          0          0          2          0
## SMAD3              635        578        516        759        756        490
## CYP1A1               0          3          0          1          0          0
## AKAP13            3305       4318       4858       5123       5809       4791
## MEFV              1342       2555       3044       3405       2470       3646
## SOCS1               43         77         60         41         28        225
## ATXN2L            1485       1846       1366       1738       1907       1757
## CD19               119        137        125        582        273         68
## ITGAL             3440       4618       5544       5837       6117       5105
## ITGAM             3807       4792       6592       5420       4159       6320
## ITGAX             2785       5581       3256       4072       3099       3731
## DNAJA2             441        564        569        886        868        745
## SIAH1               89        114         85        192        191         88
## ADCY7             1883       2192       2521       2359       2849       2699
## NOD2               213        840       1008        932        472        554
## CMTM2             1235       1871       2186       2187       1479       2868
## SF3B3              665        795        796       1123       1401        858
## PSMD7              599        660        655        804        811        576
## WWOX                39         44         34         51         39         49
## MAF                447        279        390        627        685        516
## SLC7A5             275        250        156        204        227        214
## CXCL16            1108       2246       1855       1489       1215       2345
## XAF1               573        481       1043        664        669       1834
## CD68              3167       4246       4773       4026       3564       5101
## PER1               557        712        564        223        386       2356
## NOS2                 3          1          0          0          1          1
## TRAF4               95         90         52        140        131         63
## CCL2                12          8         21         21          9          0
## CCL5              3618       3741       5033       2762       3319       1367
## CCL3                39         75        139        201        112        118
## CCR7               710       1287        378       1447       2659        850
## STAT3             2490       4611       5718       6229       4973       5567
## SOST                 0          0          0          0          0          0
## ITGA2B             306        526        757        901        583        271
## EFCAB13             25         25         15         34         28         21
## NPEPPS             526        846        893       1017        963        919
## TBX21              245        177        460        347        326        153
## COL1A1               1          0          0          0          0          3
## MRPS23             137        118        191        301        273        161
## MIR21                3         10          3          8          6          3
## RPS6KB1            323        378        282        373        560        360
## ACE                 63         24         30         47         89         43
## ERN1              1194       1220        799        899       1529       1406
## PRTN3                8         18        228         23          5          6
## PLIN5               32         69         73        101         53         87
## RETN                54         61        231         48         56         75
## CCL25                0          1          0          0          0          1
## ICAM1              796       1442       1463        989        677        823
## TYK2               941       1373       1571       2017       1668       2028
## SMARCA4            641        697        575        767        925        778
## ACP5               218        245        215        608        389        271
## JUNB             15090      21623      32473      14105       8480      23179
## CYP4F22             19         27        106         22         35         13
## JAK3               968       1519       1169       1356       1442       1719
## JUND              4256       5174       8092       3640       2418      10600
## CEBPA              647       1032       1174        806        682        774
## CEBPG              238        218        271        354        423        258
## ACP7                 0          0          0          0          0          1
## ZFP36             7073      12623      25128      13491       9928      18281
## TGFB1             4272       5579       5830       5245       3871       5257
## RPS19            10148      12296       9469      12262      11726       8689
## PSG2                 0          0          0          0          0          0
## FUT2                 1          4          3          4          2          3
## NKG7              2742       2162       6241       3094       2558       1455
## ZNF415               4          8          7          6          8          1
## LILRB2            2612       4073       3944       3733       3631       4757
## LILRA5            1721       2682       2731       2489       2634       2808
## KIR3DL1             48         83         64         82         43         48
## KIR3DL2             42         44        126         35         31         20
## SMOX                83        101        162        191         97         59
## BMP2                 3         13          4          4         10          4
## GINS1                4          5         12         12         12         12
## PLCG1              738        821        448        658       1384        741
## YWHAB             4695       5740       6504       7004       6585       6082
## PI3                216       3779        952       1450        645        631
## MMP9              1803       3463       3428       2125        888       4808
## CD40               156        170        194        384        290        161
## PFDN4               38         35         37         64         52         51
## BMP7                 0          0          0          0          0          0
## RPS21             5088       6120       4242       5604       6202       4197
## MX1                598       1003       1143       1291       1188       3351
## PFKL               995       1171       1210       1486       1482       1078
## IL17RA            3175       5869       6553       6543       5642       7414
## UBE2L3             759       1144       1110       1374       1386       1083
## TPST2              823       1129       1622       1238       1013       1103
## XBP1              1117       1173        974       1353       1565        964
## UQCR10             452        518        593        717        593        634
## SEC14L2             45         53         12         18         35         34
## APOL6              776        846       2343       1731       2296       1326
## APOL1              343        282        890        567        544        566
## TYMP              2180       2646       4719       2349       2233       5911
## BEND2               35         34         61         87         85         10
## PHEX                 9          9         16         27         18         12
## TIMP1              985       1880       1428       1928       1533       2192
## FOXP3               49         61         22         86         84         67
## MSN              16709      28453      26869      27398      22862      25207
## PGK1              5680       7930       8389       8331       7247       7350
## LAMP2             4274       7682       7847       7075       5485       8542
## CD40LG             198        164        109        272        486        173
## IRAK1             1291       1302       1506       1414       1376       1261
## COX2             62229      53770      62506      67663      59156      56414
##             GSM3308491 GSM3308492 GSM3308493 GSM3308494 GSM3308495 GSM3308496
## TNFRSF9            114        178        128        151        196        280
## ENO1              6728       5352       6845       8204       3874       5599
## PIK3CD            5532       7369       4921       6307      10881       6087
## PGD               4547       6165       3949       4296       9483       5103
## MTHFR              410        313        359        425        317        346
## TNFRSF1B         11400      17180      14738      16557      11534      13822
## PINK1              650        921        630        737       1183        735
## IFNLR1              84         50         45         78         44         28
## RUNX3             3369       2572       3742       4824       2197       2667
## SH3BGRL3          9111       9753      11323      13039       9121       8908
## CD52              5432       3302       5889       5227       1546       3581
## IFI6              4073       2685       3091       1105        917        682
## ZC3H12A            739        369        509        445        246        280
## UTP11               95        102         81         89         69        104
## JUN              15628       2833       3709       5286        155        673
## KANK4                0          0          1          0          0          0
## EFCAB7              22         20         20         28         43         30
## IL23R                2          1          2          3          2          1
## ADGRL2               0          0          0          0          0          0
## GBP3               132        140        223        129         90        123
## GBP1               855        661        966        635       1014        900
## GBP5              2362       1426       3339       1562       1806       1801
## TGFBR3             390        435        514       1080        432        510
## VCAM1                0          0          1          8          2          1
## PTPN22             294        292        255        380        315        371
## CD160              106         23        114        203         32        148
## FCGR1A             744        524        651        610       2188        707
## MCL1             19287      26363      17200      20027      34505      15398
## CTSK                59         33         58         47         25         34
## RORC                53         53         50         64         78         37
## S100A9          102839     130843      84400     109831     183422     125884
## S100A12           2218       3978       1814       2791       5132       4590
## S100A8           40067      55195      31108      41140      85571      59504
## IL6R              2660       6009       3014       4650       8606       5047
## RIT1              1081       1230       1216       1358       1632       1076
## BGLAP                6          5          6          4          8         11
## IFI16             3013       3684       2695       2987       9522       3398
## AIM2               168        110        110         76        438        106
## CRP                  0          0          0          0          0          0
## FCGR2A           12323      15166      10711      15200      28629      14692
## HSPA6             1451       1451       1434       1966       2780       1489
## FCGR3A           13763      18847      17796      17874      20546      15914
## SELL             28334      44916      36028      34436      47230      31730
## GLUL             11771      16552      13446      17052      15276      15148
## PTGS2             5680       6157       3265       5219       7823       4526
## CRB1                 2          0          1          1          1          0
## KDM5B              377        434        343        436        553        378
## IL10                 3          1          0          1          6          3
## YOD1               236        226        259        240        354        192
## HHAT                35         37         23         36         22         29
## TRAF5              411        219        253        320        196        238
## NLRP3              818        715        864        752       1436        498
## LINC01250            0          0          1          0          0          0
## RPS7             12925       7487       8507      10187       4311       7201
## RSAD2             1750       1177       1588        352        421        238
## FOSL2             3776       4480       3460       3851       6323       3159
## REL               1005        901       1018       1037        861        860
## TGFA               374        546        331        416       1388        482
## DYSF              5034       6893       3339       4324      10340       5808
## HK2                716       1282        897       1069       1603       1033
## CD8A              1519       1578        831       2759        561        547
## CD8B              1872        794        575       1156        256        266
## EIF5B              515        413        429        477        253        475
## IL1R1              202        285        141        243        739        203
## RGPD6               63         72         58         67         69         71
## IL1A                 0          0          1          1          0          0
## IL1B               789        882        311        612       1326        537
## IL37                 0          0          0          1          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             5686       3217       2070       2618       3324       3041
## NMI               1314       1949       1517       1350       2274       1536
## TNFAIP6           1234        740        222        741        923        353
## IFIH1              633        426        512        358        183        269
## SCN1A                0          0          0          0          0          0
## ABCB11               0          1          2          0          5          1
## RBM45               55         54         45         56         36         54
## FRZB                 0          0          0          2          0          0
## TFPI                 0          3          7          1          6          2
## STAT1             4113       4348       4979       4163       3338       3615
## NABP1              465        677        403        625       1473        531
## SF3B1             3561       4114       3701       4185       4783       4176
## CASP10             299        257        338        309        288        235
## CD28               747        583        625        679        285        486
## CTLA4               65         66         81         66         52         47
## ICOS               215        165        149        144         90        150
## NDUFS1             400        547        499        595        434        545
## CXCR2            10511      26024      13514      27018      54251      20350
## IRS1               193         89         95         72         82         90
## CCL20                1          2          3          1          3          0
## ATG16L1            318        217        247        287        201        225
## GPR35              115         76        134        123         30        104
## PDCD1               22         40         16         62         25          8
## PPARG                1          2          3          2          5          6
## RPL15            21925      12226      14065      17227       6609      11628
## EOMES               33         43         70        268        134         85
## CX3CR1             638        779       1020       1763        930       1373
## ACKR2                1          1          1          0          1          0
## CCR2               284        538        430        670        377        695
## CCRL2               37         24         20         21         50         33
## TLR9                46         57         48         71         95         62
## ARHGEF3           1157        789       1188       1270        556        904
## ADAMTS9              0          0          0          0          0          0
## TMEM45A              1          4          2          1         15          9
## CD80                 4          5          7          8          0          0
## CD86               814        784        965        943        141        846
## MIX23               21         14         20         31         12         17
## PLS1                24         21         20         18         16         18
## PTX3                80         30         29         23         77         88
## GOLIM4              58         83         94        111         36         94
## MYNN               266        271        260        324        300        284
## TNFSF10           2554       3732       3061       3005       5318       2691
## ADIPOQ               0          0          0          0          0          0
## SPON2              390        159        581        981        627        511
## S100P             2630       2353       1961       1468       8501       1969
## WDR1              4535       6357       6082       6964       6937       6021
## CD38               297        136        333        317        155        219
## PPARGC1A             3          4          0          2          1          8
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  2          0          0          0          0          0
## CXCL8            47185      18300      12140      30857      12756       9388
## CXCL2                8          6          7          8          6          3
## AREG                51         13         67         40         27          6
## CXCL10              52         15         18         20          1         23
## CXCL13               0          1          1          0          0          0
## SPP1                24          2         73         31         69         98
## HERC6              308        252        236        174         95        147
## NFKB1              853        845        867       1023        843        969
## SEC24B             369        408        423        519        408        384
## EGF                 11         20         45         27         56         28
## IL2                  0          1          0          2          0          0
## IL21                 0          0          2          0          0          1
## IL21-AS1             0          0          1          0          0          0
## SLC7A11             10          9          9         10         23          6
## IL15                69         69         88         80         33         72
## EDNRA                0          0          0          0          0          0
## TLR2              3061       3928       2351       3664      23267       3296
## FGB                  0          0          0          0          0          0
## DDX60              588        546        645        361        218        305
## SPCS3             1628       1886       1648       2223       1880       2257
## TLR3                 2          3          8         20          3         13
## OSMR                16         36         39         28         29         21
## GZMK               348        212        637       1237        239        567
## GZMA               652        499        854       1817        809        951
## ANKRD55             65         80         33         71         73         75
## CENPK               29         51         84         90         35         56
## CAST              2284       2163       2714       3803       1560       3301
## ERAP1              896       1095       1336       1899        673       1398
## ERAP2             1629        105       1782       1667        856       2661
## TNFAIP8           1431       1455       1166       1592       1032       1159
## CSF2                 1          1          0          0          0          1
## IL5                  0          0          0          0          0          2
## IL13                 0          1          0          0          0          0
## IL4                  2          9          1          1          1         15
## CD14              9505      10349       7362       9094      10541      12260
## CSNK1A1           1254       1811       1392       1812       1793       1585
## PPARGC1B           132        102        183        116         33         88
## TNIP1             4457       5020       4041       4725       4018       4453
## ATOX1              195        163        178        195        116        160
## FAXDC2             109        113        198        171        229        143
## IL12B                0          0          0          1          1          0
## MIR146A              0          0          1          0          1          0
## PDLIM7            1293       1783       1370       1766       1795       1511
## SERPINB1          3751       4827       4122       5084      10371       4691
## SSR1              1792       2431       2189       2515       1793       2361
## CD83               741        298        407        256         45        569
## SOX4               181        138        294        236         40        151
## CMAHP               85         57         59         56         52         84
## HLA-A            41218      49804      47316      40709      39041      40021
## HLA-C            73116     116043      77740      83909     137823      87552
## HLA-B           103057     111782      99416     122512     117014      90833
## MICA               149         80        106        110         63         82
## LTA                 92         55         62         66         44         42
## TNF                168        182        351        179         32        227
## HLA-DRB1          3555       3575      11700       5443        874       4662
## HLA-DQB1          3116       1142       7120        997        370        852
## PPARD              325        364        269        317        192        286
## CCND3             5069       3775       4254       5115       8234       3151
## VEGFA              156        135        245        137         58        123
## RUNX2              404        543        526        513        520        469
## IL17A                0          0          0          2          0          0
## IL17F                0          0          0          0          0          0
## PRDM1              269        586        436        749        973        402
## ATG5               307        335        386        408        281        344
## TRAF3IP2           243        187        168        246        149        170
## NCOA7              294        335        302        316        281        367
## SGK1              1974       2413       1414       1897        550       3748
## IFNGR1            1768       3050       2207       3699       8385       3042
## TNFAIP3           6664       1554       3033       2915       1727       1598
## SOD2             44677      62870      31629      46558      65865      45492
## LPAL2               11          5         11         12          6         13
## PLG                  0          0          0          0          0          0
## CCR6                70         84         95        149        100         68
## RAC1              2183       3111       2820       3532       2966       2499
## ZNF316             653        574        805        832        264        624
## AHR                834        853        867        670        326        884
## IL6                  9          3          2          3          2          2
## TOMM7             2811       2326       2362       2760       1149       1955
## CYCS               618        386        572        589        283        495
## AQP1                 1          1          1          2          8          3
## NT5C3A             737        812        746        691        706        640
## EGFR                 0          0          0          0          0          0
## CD36              1699       1947       2278       1659        387       2459
## SAMD9             1836       2489       1737       1699       2323       1630
## SERPINE1             6          6         17          8         47          9
## CUX1              1605       1603       1533       1437       1595       1556
## PSMC2              281        301        339        400        208        337
## NAMPT            44901      67492      35415      55157      95725      48109
## HYAL4                2          0          0          0          0          0
## LEP                  3          6          0          4          3          6
## CALD1                5         12         32         14         37         18
## BRAF               611        727        569        585        806        576
## EZH2                68         42         38         66         56         43
## DNAJB6            1170       1538       1360       1687       1816       1300
## CSMD1                5         12          0          5          0          0
## CTSB              4785       5605       5911       6221       1741       5444
## EGR3               365        529        161        480       2193        857
## TNFRSF10A          191        114        143        133         89        132
## BNIP3L            1737       2751       1938       2353       2458       2362
## DUSP4               83         92         93         62         24         23
## NRG1                67         56        126        140         28         35
## RPL7             14783       9636      10228      11755       5108       8409
## IL7                 15         18         10         19          7          9
## GEM                  2          0          0          2          0          0
## MYC                503       1021        644        782        505        614
## GPT                  2          1          2          1          0          2
## JAK2               796        947        902        871       1401       1055
## CD274              259        150        131        105        284         93
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              1          1          2          2          1          3
## TTC39B             153        112        128        155         93        124
## IFNA1                0          0          0          0          0          0
## TEK                 27         24         49          8         23         30
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              241        209        217        250        108        205
## ANXA1             5345       5988       8072       5655       3808       5933
## ERP44             1166       1255       1365       1365       1102       1333
## ZNF483              23         28         37         38         15         30
## TNFSF15              2         12          5          3          3          8
## TLR4              3563       8042       3351       5092      10266       5767
## PTGS1              409        489       1070        754        994        622
## HSPA5             5661       3515       4449       5245       8320       5330
## FNBP1             3203       3767       3485       4141       2743       3248
## CARD9              164        116        189        199         48        175
## TRAF2              127        107         91        147         66        113
## CLIC3              108         40        111        218        119         86
## IL2RA              162        128        184        101         95        114
## GATA3              254        502        382        285        161        340
## VIM              15796      21782      19332      19336       9350      14897
## CREM               143        150        171        186        158        145
## DKK1                 0          0          0          0          2          0
## MBL2                 0          0          0          0          0          0
## SAR1A              604        779        754        841        699        671
## PRF1              1170       1335       2350       5814       2710       1764
## ZMIZ1             1763       2552       2890       2417       2069       2068
## IFIT3            11066       6249       7338       2509       3760       2257
## TALDO1            7565      10266       8153      11379      11910       8751
## IGF2                 0          0          0          0          1          0
## INS-IGF2             0          0          0          0          1          0
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1302       1259       1203       1764       1234       1110
## TRIM22            2715       2666       3099       2377       5997       2072
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          1          0          0          0
## SLC1A2               1          3          1          1          0          1
## FOSL1               34         64         38          2         15         25
## CCND1                8          1          4          7          9          7
## JRKL                71         80         58         89         66         80
## MMP7                 0          0          0          0          0          0
## MMP1                 0          0          0          1          1          1
## MMP3                 0          0          0          0          0          0
## CASP1             2410       2901       2897       3128       4325       3182
## DLAT               167        171        166        224         97        162
## IL18                69        104         92         99         94         94
## CD3E              4674       3063       2671       4046       1320       2087
## MCAM               230        277        272        241        251        255
## WNK1              2968       4278       3321       4311       3406       4027
## TNFRSF1A          2523       4766       2641       4777       8800       3637
## GAPDH            19168      18282      15577      21054      11700      17992
## CD4               4157       3552       4573       4546       1085       4272
## SLC2A3            9897      14275       8390       7561      15719       9735
## CLEC4D             420        858        195        316       1835        404
## KLRB1             1012        385        997       1321        849        700
## CD69              2368        809       1261       1027        353        824
## CLEC2B            1376       2090       1572       1525       1552       1691
## OLR1                14          7          4          6        169         80
## ABCD2              209        184        160        205        100        156
## LRRK2             4923       8943       5011       6469      13084       7582
## VDR                254        465        372        443        393        417
## TMBIM6           11135      14678      11670      15340      16702      12810
## PFDN5             4537       3094       3349       4124       1776       3130
## SP7                  0          2          0          0          0          0
## MUCL1                0          0          0          0          0          0
## CD63              2319       2499       2964       2879       3036       2740
## SUOX               811       1321        989       1255       1222       1113
## RPS26             5370        656        793       4178        455       5074
## RPL41            11320       7765       8213       9449       3897       7232
## IL23A               49         38         33         38         18         20
## DDIT3              461        319        452        370        630        394
## IFNG                23          4         15         31          4          4
## IL22                 0          0          0          0          0          0
## LYZ              90993      37921      76361      64816      12163      53039
## CAPS2                2          5          3          9          3          1
## SYT1                 4          2          1          0          1          2
## BTG1             10907      10167       9340      10745       7783       6858
## HCAR3             3420       2581        793       2535       7171       3763
## GJB2                 3          3          0          0          0          0
## GJB6                15         12         14         11         13         13
## TNFSF11              0          7          2          6          0          5
## TPT1             81553      56267      59037      66597      34403      49019
## LMO7                97         56         44         70         52         84
## TNFSF13B          2783       2921       2330       2062       2567       1731
## LAMP1             2614       3042       2640       2940       2616       2434
## PSME2             1527        952       1893       1374        425       1119
## GZMB               723        476        936       1733        886        621
## RPL36AL           2813       2064       2534       2406       1449       1861
## PYGL              4371       6818       3588       5963      10972       6018
## HIF1A             1932       2035       2293       1964       2494       1644
## FOS              61601      25824      17911      25173      13787       8408
## JDP2               509        843        855        714       1429        703
## NOXRED1              6          8          5          6         26          6
## SERPINA1         21563      31132      26527      21980      38479      23307
## CDC42BPB           258        175        248        250         91        245
## PLA2G4D              0          0          0          0          0          0
## TRIM69               9         17         14         12         17         11
## SLC51B               0          0          0          0          0          0
## SMAD3              729        485        679        700        268        504
## CYP1A1               1          3          0          0          0          1
## AKAP13            3651       4231       3570       4594       8977       3893
## MEFV              2131       3689       2708       3427       4104       2761
## SOCS1               92        137         82         83         56         39
## ATXN2L            2247       1502       1619       1842        934       1315
## CD19               239        122        141        179        100         89
## ITGAL             4747       4449       5069       5924       3948       5029
## ITGAM             4475       5565       4342       4577       7539       5356
## ITGAX             4109       3336       4383       4663       4439       4167
## DNAJA2             555        607        513        660        618        594
## SIAH1               91        103        131        134        142         95
## ADCY7             2405       1858       2130       2618       1968       2423
## NOD2               818        892        751        706       1399        419
## CMTM2             1625       2645       1689       2214       4318       2543
## SF3B3              952        831        788       1114        493        766
## PSMD7              627        637        656        758        431        614
## WWOX                49         35         50         55         31         36
## MAF                477        530        922        525        341        396
## SLC7A5             248        214        210        268        261        163
## CXCL16            1667       2543       1912       1466       3205       1510
## XAF1              1575       1000       1535        693        354        586
## CD68              3609       3369       5302       3953       1190       3748
## PER1               840        436        764        648       1377        325
## NOS2                 0          2          0          2          3          0
## TRAF4              137         64         96         81         33         52
## CCL2                29         19          1          7          2         15
## CCL5              2167       1863       2640       6581       2198       2203
## CCL3               251         66        104        273         44         77
## CCR7              1274        803        424        849        645        511
## STAT3             3273       5437       3743       5376       9643       4817
## SOST                 0          0          0          0          0          0
## ITGA2B             164        199        466        373        689        336
## EFCAB13             33         16         18         17         16         23
## NPEPPS             620        994        650        925       1368        857
## TBX21              205        163        275        542        300        269
## COL1A1               0          1          1          0          1          0
## MRPS23             125        138        156        224         94        167
## MIR21                4          6          7          3         17         11
## RPS6KB1            353        343        318        403        333        360
## ACE                 24         54         73         42          9         34
## ERN1               935       1128        934       1247       2069        652
## PRTN3                4          6         10          8         32         20
## PLIN5               85        104         59         92        301         58
## RETN                88         41         35         52        247        192
## CCL25                1          0          1          1          0          0
## ICAM1             2085       1366       1585       1588        949       1339
## TYK2              1223       1780       1303       1757       1835       1691
## SMARCA4            758        613        653        743        320        570
## ACP5               264        251        249        264        135        288
## JUNB             38070      32523      30507      28110      11137      16533
## CYP4F22             11         19         67         42          6         67
## JAK3              1771       1469       1224       1776       3033       1537
## JUND             13577       7980       7069       6051       3005       3258
## CEBPA             1056        925       1012        957        723       1028
## CEBPG              236        212        294        278        142        259
## ACP7                 0          2          0          1          1          0
## ZFP36            32610      18711      17204      16607       7229       8528
## TGFB1             5180       5537       5745       5407       3221       3712
## RPS19            16606       9151      10954      11625       4983       9201
## PSG2                 0          0          0          0          0          0
## FUT2                 1          1          3          5          1          3
## NKG7              2441       1547       2993       7526       3657       2799
## ZNF415               3          8          5          5          9          8
## LILRB2            3874       3765       4620       4159       3372       4317
## LILRA5            1796       2337       2681       2083       2398       2455
## KIR3DL1             42         73         63         70        185         53
## KIR3DL2             15         20         57         48         93         35
## SMOX                66         78        109        117        214         93
## BMP2                 4          5          5          2          8         10
## GINS1               11          7          4         18          5          7
## PLCG1             1077        613        632        804        526        677
## YWHAB             5078       6208       5516       6232       5366       5859
## PI3               1750       1390       1125       2356        256       1664
## MMP9              1445       4378        863       1661       7384       4667
## CD40               175        143        184        185         97        111
## PFDN4               55         53         45         57         29         49
## BMP7                 0          0          0          0          0          0
## RPS21             8161       4925       5134       5964       2244       4335
## MX1               3559       2273       2765       1440        609        457
## PFKL              1263       1040       1306       1334        582       1032
## IL17RA            3822       7013       4511       5932      11676       5328
## UBE2L3             842       1024       1020       1243        846        949
## TPST2             1087       1047       1156       1460       1191       1024
## XBP1               862        852       1116       1251        917       1016
## UQCR10             556        514        574        682        412        507
## SEC14L2             78         29         15         36         13         21
## APOL6             1310       1258       1455       1275       1807       1339
## APOL1              567        587        845        553        538        591
## TYMP              4342       4196       4684       4328       1741       2725
## BEND2               16         27         39         79        120         56
## PHEX                 4         17          5         13          6         20
## TIMP1             1438       2157       1880       2347        695       1310
## FOXP3              103        137         93        115         36         74
## MSN              20898      24097      24811      30794      24517      22761
## PGK1              7204       7378       7688       8618       9731       8209
## LAMP2             5130       8679       6047       7074       9561       7018
## CD40LG             130        207        134        207        114        149
## IRAK1             1504       1173       1552       1545        970       1200
## COX2             67325      44572      57346      77986      31634      41950
##             GSM3308497 GSM3308498 GSM3308499 GSM3308500 GSM3308501 GSM3308502
## TNFRSF9             84         98        116        120         77        163
## ENO1              6223       6337       6559       5928       5945       5808
## PIK3CD            4545       7024       7566       9163       6008       6140
## PGD               3182       5495       5563       5988       4343       5736
## MTHFR              633        356        428        410        432        403
## TNFRSF1B         12067      11644      15568      14207      15320      15295
## PINK1              426        729        939        814        642        592
## IFNLR1              39         44         63         69         49        183
## RUNX3             2676       2341       3933       3226       3128       3490
## SH3BGRL3          8825       9496      10467       9566      10460       9885
## CD52              4714       4588       4323       3734       4942       3285
## IFI6              3668        931        676        650        546       5266
## ZC3H12A           1084       1133        511        355        575        605
## UTP11               47         48        114        132         70         76
## JUN              26857      20547       7995        425        831        452
## KANK4                0          0          0          0          0          0
## EFCAB7              21         20         35         31         25         25
## IL23R                0          4          0          1          9          0
## ADGRL2               0          0          0          0          0          0
## GBP3               392        193        160        277        215        344
## GBP1              2909        624        721       1117        805       5502
## GBP5              8742       1879       1683       2881       2619      16953
## TGFBR3             264        414       1153       1075        556        770
## VCAM1                1          2          6          5          2          1
## PTPN22             199        226        428        645        362        338
## CD160               45         92         85        161        130         46
## FCGR1A            2145       1071        729        372       1484       6900
## MCL1             29174      29729      20854      22808      17720      25655
## CTSK                89         56         50         39         51         51
## RORC                22         24         30         62         61         18
## S100A9           74654     183955     152129     122056     141519     191542
## S100A12           1541       6302       3344       3434       3239       3907
## S100A8           28075      75923      55500      50295      52054      78905
## IL6R              2745       4242       5010       6627       3422       3575
## RIT1               967       1355       1349       1288       1194       1336
## BGLAP                7          9          8          6          4          6
## IFI16             1904       2078       2700       3746       2821       6425
## AIM2               132        194        113        201         44        360
## CRP                  0          0          0          0          0          0
## FCGR2A            8502      14723      14054      14657      15554      17777
## HSPA6             1031       1238       1437       5274       2200       2781
## FCGR3A           12948      16597      15728      23538      18625      23442
## SELL             30121      42607      37905      37742      24604      55456
## GLUL             14016      17207      20759      12462      18957      18304
## PTGS2            14686      21048       8237       7604       1840       1500
## CRB1                 0          0          1          3          0          0
## KDM5B              416        473        437        603        418        404
## IL10                 3          2          3          1          7          4
## YOD1               227        169        220        262        248        342
## HHAT                44         49         41         32         17         21
## TRAF5              350        324        377        415        483        282
## NLRP3             1626       1063        855        614        618        902
## LINC01250            0          0          1          0          2          0
## RPS7              9052       8416       8207       6533      12496       7501
## RSAD2             2695        332        151        238         83       7178
## FOSL2             3187       4228       4528       3216       2763       3204
## REL                987        934       1188       1276       1118       1171
## TGFA               299        530        521        721        441        689
## DYSF              3311       7138       5960       7420       4995       9095
## HK2                819       1127        980       1885        456        890
## CD8A               335       1005        930       2953       1134       1990
## CD8B               218        742        481        786        760        659
## EIF5B              398        454        587        602        430        427
## IL1R1              130        277        285        240        348        227
## RGPD6               50         42         92        101         92         49
## IL1A                23          6          0          1          2          0
## IL1B              6088       3296        848       1149        644        377
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             9938      11509       3120       2307       3214       4342
## NMI               1422       1360       1149       1482       1933       3066
## TNFAIP6            709        758        659        578        445       1291
## IFIH1              770        395        275        422        416        981
## SCN1A                0          0          0          0          0          0
## ABCB11               1          1          1          1          0          0
## RBM45               46         33         76         65         59         74
## FRZB                 0          0          0          1          1          0
## TFPI                 5          5          6          5          7          2
## STAT1             5677       2978       2938       4727       3008      11528
## NABP1              712        959        845        886        668        718
## SF3B1             4151       4842       4940       4604       4768       5402
## CASP10             405        276        329        433        327        405
## CD28               887        694        471        707        745        388
## CTLA4              130         54         70         70        134         92
## ICOS               203        135        124        201        494        217
## NDUFS1             348        339        535        644        416        522
## CXCR2            11020      16361      20346      23947      21010      19354
## IRS1                78        122         72         28         76         49
## CCL20                7         16          1          1          1          2
## ATG16L1            302        241        318        306        367        292
## GPR35              115         77         86        105        116        116
## PDCD1               16         33         51        108         25         50
## PPARG                1          4          0          7          4          8
## RPL15            15911      13315      12406       9962      16630      11180
## EOMES               55        118        128        487        126        109
## CX3CR1             531        797       1522       4250        841        951
## ACKR2                3          2          0          4          0          0
## CCR2               363        516        743       1610        517        612
## CCRL2               81         61         47         40         55         28
## TLR9                46         48         89        116         86         91
## ARHGEF3           1285        961       1047       1362       1149       1215
## ADAMTS9              0          0          0          0          1          0
## TMEM45A              2          7          4          2          0          2
## CD80                 7          6          3          6          6         10
## CD86              1074        674        920        707        586        991
## MIX23                9         17         32         20         40         31
## PLS1                10         21         22         15         16         13
## PTX3               213        152         65         24         34         54
## GOLIM4              54         61        140        141         67         80
## MYNN               337        331        392        346        336        381
## TNFSF10           3005       2399       2334       4176       2407       5791
## ADIPOQ               0          0          0          0          0          0
## SPON2              397        182        437        382        244        354
## S100P             1022       4784       4430       3629        224       1586
## WDR1              4131       4748       6153       6722       5452       5839
## CD38               321        188        177        257        241        288
## PPARGC1A             2          8          3          4          2          0
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          0          0          0          0
## CXCL8            69671     124095      56677      13508       7177       7053
## CXCL2               98        108         14          0          1          3
## AREG               143        106         27          0         17         76
## CXCL10             102         30         23         24          4         69
## CXCL13               0          0          0          2          1          0
## SPP1                20         20         67         40        123         25
## HERC6              249        157        162        218        190        283
## NFKB1              885       1037        915       1298       1212        989
## SEC24B             399        375        407        630        479        459
## EGF                 37         48         29         46         42         22
## IL2                  1          0          0          0          0          0
## IL21                 1          3          0          2          1          0
## IL21-AS1             1          2          0          4          1          1
## SLC7A11              7         14         11         16         12         14
## IL15               118         78         96         83         60        100
## EDNRA                0          0          0          0          0          0
## TLR2              3174       4196       3679       4951       4251       7038
## FGB                  0          0          0          0          0          0
## DDX60              688        236        277        520        225       1770
## SPCS3             1260       1626       2394       2425       1894       1834
## TLR3                 5          6         14         42          2         14
## OSMR                25         20         29         29         27         46
## GZMK               270        694        652        875        838        332
## GZMA               452        730       1602       1517       1002        665
## ANKRD55            117         50         37         58         80         47
## CENPK               14         20         66          8         26         93
## CAST              2150       2126       4341       3180       2756       2334
## ERAP1             1413       1183       1677       2012       1600       1823
## ERAP2             1890       2241       1398       1743       1443       2202
## TNFAIP8           1217       1158       1509       1742       1564       1289
## CSF2                 0          0          0          0          1          0
## IL5                  0          0          0          0          0          0
## IL13                 0          0          0          0          0          0
## IL4                  2          3          6          2          0          0
## CD14              6626      10464      14154       7389      10472      12024
## CSNK1A1           1254       1341       1656       2204       1510       1741
## PPARGC1B           222        125         91         99         70        141
## TNIP1             3937       5094       4894       4463       5752       4593
## ATOX1              194        172        167        175        184        224
## FAXDC2             220        220        208        164        203        134
## IL12B                1          0          0          1          2          1
## MIR146A              0          0          0          0          0          0
## PDLIM7            1099       1864       1713       1749       2089       1840
## SERPINB1          3668       4851       4986       4644       5738       7715
## SSR1              1734       1704       2584       2141       1851       2290
## CD83              1343       1260        458        115        340        331
## SOX4               209        110        146        188         92         79
## CMAHP               98         76         87        107        172        127
## HLA-A            48295      33555      22870      40696      40182      45834
## HLA-C            51315      89602      73394      85009      84835     112204
## HLA-B           104537     104188      76822      74684      98411     153881
## MICA               168        167        123        152         45         86
## LTA                 59        123         43         73         62         30
## TNF                233        225        415        168        189        199
## HLA-DRB1          8620       3181       3363       2549       3324       5223
## HLA-DQB1          4701        308       3186        269       2241        713
## PPARD              319        200        285        352        387        326
## CCND3             3848       3725       3943       3606       4341       5425
## VEGFA              220        202         99        122         97        105
## RUNX2              427        347        467        497        490        495
## IL17A                0          0          1          1          0          0
## IL17F                0          0          0          0          0          0
## PRDM1              637        289        461       1112        546        961
## ATG5               385        293        409        355        431        470
## TRAF3IP2           223        183        159        149        200        169
## NCOA7              339        283        364        405        283        532
## SGK1              4433       4428       2884       3845       4281       1689
## IFNGR1            1446       2038       3066       4256       3666       3515
## TNFAIP3          26895      20913       2206       1049       2462       4777
## SOD2             40590      57829      55811      40057      47013      68387
## LPAL2               11         17         22         42         24         14
## PLG                  0          1          1          1          0          0
## CCR6                93         71         82        153        130         50
## RAC1              1678       2564       3028       2793       2967       2856
## ZNF316             992        777        783        729        982        638
## AHR               2635        932       1338        524       1149       1273
## IL6                 21         14          5          0          6          0
## TOMM7             2035       1975       2367       1558       2638       1793
## CYCS               808        796        573        568        422        508
## AQP1                 3          7          5          3          2          2
## NT5C3A             660        721        730        703        670       1303
## EGFR                 0          0          0          0          0          0
## CD36              2881       2970       2042       1903       1729       1371
## SAMD9             2140       1502       1862       2015       1305       2999
## SERPINE1            21         21         27         15         17          5
## CUX1              1653       1655       1577       1457       1096       1464
## PSMC2              268        241        356        472        314        387
## NAMPT            42289      62601      56675      41178      67250      94769
## HYAL4                1          0          0          0          0          0
## LEP                  0          1          1         16          1          3
## CALD1               21         52         21          9         22         11
## BRAF               593        666        713        765        636        598
## EZH2                70         73         58         67         69         68
## DNAJB6            1038       1195       1776       1274       1391       1430
## CSMD1                8          0          1          2          2          4
## CTSB              6091       4796       5292       4851       4968       5469
## EGR3              1345       1118       1764        109        922        822
## TNFRSF10A          165        161        142        167        191        154
## BNIP3L            1452       1559       2416       2158       2047       2046
## DUSP4              124        101         31         24         31         54
## NRG1               102         93         79         41        235         69
## RPL7             11367       9678       9122       7097      11744       7802
## IL7                  9         12         18         14         24         24
## GEM                  5          6          0          0          0          0
## MYC                264        302        545        632       1557        902
## GPT                  5          1          0          3          1          1
## JAK2              1288       1212       1098       1479        767       1661
## CD274              609        232        103        175        334       1363
## IL33                 0          0          0          0          1          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              1          2          5          2          7          0
## TTC39B             196        145        137        211        249        150
## IFNA1                0          0          0          0          0          0
## TEK                 26         28          9         10          3          9
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              197        224        262        227        203        242
## ANXA1             7085       5621       8016       5345       4941       7476
## ERP44             1353       1262       1564       1079       1055       1780
## ZNF483              40         28         27         57         21         24
## TNFSF15              4          7          5         11          1          4
## TLR4              3878       5176       8582       7123       5374       8334
## PTGS1              956       1051        785        760       1049        582
## HSPA5             6400      10367       8092       3571       5650       5519
## FNBP1             2133       2630       3573       3941       3312       3373
## CARD9              245        163        166        209        133        167
## TRAF2              129        102        125        148        150        116
## CLIC3               56         55         97        133         92         61
## IL2RA              132         78        127         89        118        140
## GATA3              343        286        313        396        294        171
## VIM              16362      17146      17569      15163      15268      14487
## CREM               182        128        210        140        195        249
## DKK1                 0          1          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              769        575        874        998        867        938
## PRF1              1125        387       3081       3467       1695       1920
## ZMIZ1             2234       1738       2186       2220       1915       2258
## IFIT3            15270       2849       1741       2704       1680      18101
## TALDO1            5787       8908       9105       9570       9430       9255
## IGF2                 1          0          0          0          0          0
## INS-IGF2             1          0          0          0          0          0
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1000       1108       1311       1445       1364       1368
## TRIM22            3423       1868       1879       2015       1833       9534
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          0          0          0          1
## SLC1A2               0          1          0          2          0          3
## FOSL1              118        161         82          3         36         33
## CCND1               10          8          4          7         12         10
## JRKL                63         82         72        148         83         48
## MMP7                 0          0          0          0          0          0
## MMP1                 3          0          3          5          4          5
## MMP3                 0          0          0          0          0          0
## CASP1             3076       2546       2850       2786       2842       5908
## DLAT               145        123        178        224        176        172
## IL18                91         40        106         67         50         77
## CD3E              3121       3228       2939       3225       3226       2589
## MCAM               222        244        271        232        264        199
## WNK1              3150       3684       4016       4525       2934       2684
## TNFRSF1A          2093       2861       3914       5234       4476       3606
## GAPDH            17375      17952      20679      14568      16738      16839
## CD4               4736       3390       3849       3655       2532       3313
## SLC2A3            6606      15235      10424       7398       8799       6683
## CLEC4D             146        416        858        456        329        461
## KLRB1              496        717        786        491        968        309
## CD69              5064       4649        910        288       1031       1061
## CLEC2B            1791       1982       2020       1411       2048       3157
## OLR1                 4         46         25         24         42          6
## ABCD2              228        208        160        330        190        136
## LRRK2             5402       6651       7262      11301       4853      10323
## VDR                319        368        478        498        389        293
## TMBIM6           10443      13070      14312      13406      12421      12329
## PFDN5             3970       3256       3217       2448       4854       2877
## SP7                  0          0          0          0          0          0
## MUCL1                0          0          0          0          0          0
## CD63              2351       2654       3236       2367       2943       3705
## SUOX               666        857       1187       1162        922       1010
## RPS26             7431        670        713       2478       4527       3024
## RPL41             8626       7639       7096       5305      10403       6340
## IL23A               65         49         27         31         53         30
## DDIT3              583        805        496        287        536        620
## IFNG                36         26         30         37          6          7
## IL22                 0          0          0          0          0          0
## LYZ              85835      59545      49952      71646      42042      80945
## CAPS2                6          7          3          5          4          2
## SYT1                 0          1          4          0          0          1
## BTG1             12554      11253       9337       7406       6550       7497
## HCAR3             3551       6767       3455       2309       2596       3671
## GJB2                 3          2          0          0          0          0
## GJB6                15         26         20          2         17          2
## TNFSF11              3          2          4          4          2          0
## TPT1             60647      55288      52077      38154      71958      44954
## LMO7                82         64         57         85         62         40
## TNFSF13B          2128       2676       2586       1788       2505       5266
## LAMP1             2526       2941       3217       2813       2397       2857
## PSME2             2387       1082        999       1107       1193       3152
## GZMB               749        286       1136        815        614        672
## RPL36AL           2489       2062       2252       1848       2678       1739
## PYGL              2642       8984       6109       6004       4801       7277
## HIF1A             3196       2238       2748       1802       2529       3992
## FOS              71368      64992      54311      16371      10567       5227
## JDP2               559        647        784        686        624        686
## NOXRED1              5          5         13          4         11         12
## SERPINA1         20709      24162      20989      24228      23581      30445
## CDC42BPB           387        268        236        223        140        290
## PLA2G4D              0          0          0          0          0          0
## TRIM69              12         11         23         12         15         31
## SLC51B               0          0          0          0          0          0
## SMAD3              572        603        714        740        807        529
## CYP1A1               0          0          0          1          0          0
## AKAP13            4477       3249       4951       6183       3390       6201
## MEFV              1753       2291       2678       4105       2915       4327
## SOCS1              146         89         51         33         61        130
## ATXN2L            1951       1665       1606       1478       1851       1527
## CD19               134        166        191         97        214        347
## ITGAL             4440       4424       6062       7061       4200       5698
## ITGAM             3592       6238       7251       6264       4400       7103
## ITGAX             3740       5799       5135       4611       7420       6285
## DNAJA2             573        519        621        870        609        640
## SIAH1              127         83         95        212        126        119
## ADCY7             2513       2197       2882       2926       1931       2456
## NOD2               714        489       1247       1031       1017       2140
## CMTM2             1092       2008       3024       2849       2546       1844
## SF3B3              840        933        883       1085        796        768
## PSMD7              574        516        711        706        724        650
## WWOX                48         23         41         43         39         32
## MAF                523        422        694        629        554        381
## SLC7A5             196        216        232        152        277        225
## CXCL16            2232       2163       3028       1033       3421       1706
## XAF1              1878        708        652        659        557       4618
## CD68              4001       2990       3551       3576       2503       4260
## PER1              1544        590        547        189        608        929
## NOS2                 1          2          2          0          2          0
## TRAF4              104        118        110         68         89         82
## CCL2                21         14         34          1          4         10
## CCL5              1517       3260       5144       5590       3596       3206
## CCL3               505        620        121         62        144         24
## CCR7              1134        722        484       1066       1316        605
## STAT3             3083       4086       4639       5966       4601       6594
## SOST                 0          0          0          0          0          0
## ITGA2B             523        692        296        390        974        346
## EFCAB13             27         22         22         19         16         22
## NPEPPS             672        797        954       1219        932        969
## TBX21              181        149        494        755        330        445
## COL1A1               3          1          0          1          1          2
## MRPS23              98         82        200        233        181        155
## MIR21                7          3          6          5          5          2
## RPS6KB1            312        317        345        460        382        382
## ACE                 30         32         21         46         33         46
## ERN1              1116        889       1171       1105       1032        739
## PRTN3               15          8         14          9         18          9
## PLIN5               97        161        147        109        187        115
## RETN               410        210        100         87         49         52
## CCL25                0          1          1          0          4          0
## ICAM1             3518       3516       2042        874       2341       2664
## TYK2              1462       1504       1890       2461       1641       1601
## SMARCA4            646        615        800        848        648        618
## ACP5               213        258        303        228        387        478
## JUNB             36032      31096      42777      18508      35480      16448
## CYP4F22             70         16         14         30         36         61
## JAK3              1945       2024       1877       2041       3259       2702
## JUND             22156      17497       7978       2938       4834       4213
## CEBPA              680        695        828       1221        651        861
## CEBPG              267        164        239        403        231        289
## ACP7                 1          0          0          0          1          0
## ZFP36            41583      40258      18163      15631      10266      14721
## TGFB1             4364       5211       4765       5079       5173       5464
## RPS19            12466      10285       9561       7612      13571       8779
## PSG2                 0          0          0          0          0          0
## FUT2                 1          3          2          3          2          1
## NKG7              2024       2257       4821       4524       3079       3467
## ZNF415               4          2          3          3         15          9
## LILRB2            4437       4372       5012       3812       5536       5507
## LILRA5            2012       3685       2974       3935       6137       3272
## KIR3DL1             21         68        105         89         19         20
## KIR3DL2             43         19        108         60         12         21
## SMOX               159        146        117         97        149         57
## BMP2                 5          9          9          3          5          0
## GINS1                9          2          9          7          8          4
## PLCG1              870        724        731       1063       1027        534
## YWHAB             4378       5575       7203       6036       4542       6690
## PI3               1036       1016       1625        750       3044        947
## MMP9               479       2222       3604       4607       1378       1901
## CD40               308        184        184         96        183        204
## PFDN4               49         37         48         45         44         46
## BMP7                 0          0          0          0          0          0
## RPS21             5735       4718       4451       3397       6614       3978
## MX1               2401       1283        529        977        463       4615
## PFKL              1159        928       1185       1245        980       1138
## IL17RA            3861       5270       6098       8597       4932       7254
## UBE2L3             719        796       1121       1094        921       1066
## TPST2              832       1310       1374       1408       1303       1072
## XBP1               923        817       1089       1397       1303        936
## UQCR10             495        449        635        527        606        493
## SEC14L2             42         44         18         20         35         23
## APOL6             2697        903       1221       2128        996       4991
## APOL1             1125        512        683        658        569       1641
## TYMP              5191       3844       3548       4231       4013       6892
## BEND2               99         72         73         69         69         23
## PHEX                 9         12         14         23          8          0
## TIMP1             1192       1414       2649       1576       2028       1137
## FOXP3               92         67         68        120         77         39
## MSN              17075      23255      25385      24401      19566      24745
## PGK1              7002       8361       9062       6494       8188       8663
## LAMP2             4364       6126       7185       6618       5453       7363
## CD40LG             177        134        163        268        175         61
## IRAK1             1696       1236       1567       1313       1376       1488
## COX2             52863      43316      49415      43591      42967      40652
##             GSM3308503 GSM3308504 GSM3308505 GSM3308506 GSM3308507 GSM3308508
## TNFRSF9            153        232         91        135        279        160
## ENO1              6676       7534       7077       6100       6327       7345
## PIK3CD            8297       6481       6150       7949       7804       9212
## PGD               6622       6641       5677       6586       4461       4453
## MTHFR              358        325        296        354        455        497
## TNFRSF1B         16649      13431      13391      12488      12305      13145
## PINK1              794       1053        687        836        837        785
## IFNLR1              43         17         40         27         57         39
## RUNX3             2803       2347       2528       1916       3403       3193
## SH3BGRL3         10008      12800       9026       9492       8824       9180
## CD52              3149       3547       3833       3179       3580       4702
## IFI6               864       1521       4704       1762        623       1167
## ZC3H12A            419        417        283        328        438        388
## UTP11              124        114         90         94        125        215
## JUN               4358       4386        188       1087       1598        303
## KANK4                0          0          0          0          0          0
## EFCAB7              20         20         25         18         36         45
## IL23R                2          1          2          1          1         21
## ADGRL2               0          0          1          0          1          0
## GBP3               276        176        131        208        328        595
## GBP1               953       1418       1274        998       1183       2012
## GBP5              2861       2578       2179       2214       3335       4844
## TGFBR3             614        393        439        259        697        655
## VCAM1                1          0          4          1          6          2
## PTPN22             415        453        333        321        454        611
## CD160              158         52         45         55         85        178
## FCGR1A            1085       1458       1538        752       1348        778
## MCL1             22890      30075      23691      17347      21278      22706
## CTSK                57         80         28         52         68         54
## RORC                46         17         32         14         74        290
## S100A9          170797     166713     179161     154068     107188     102280
## S100A12           7108       5355       6273       4833       3556       4366
## S100A8           69459      68573      74911      68700      40159      39610
## IL6R              4525       4702       5214       5122       4449       6287
## RIT1              1422       1481       1064       1210       1143       1160
## BGLAP                8          8          7          6         11          4
## IFI16             3883       3799       4916       3370       3449       5003
## AIM2               200        141        233        192        210        231
## CRP                  0          0          0          0          0          0
## FCGR2A           17439      14330      14482      17933      16627      14082
## HSPA6             2184       2195       1537       1734       1664       2195
## FCGR3A           11434      16009      15859      20344      13783      18872
## SELL             33586      30457      28827      35589      36572      36612
## GLUL             17240      20494      12747      12596      14334      10757
## PTGS2            12879       8593       1852       6688      16253      12228
## CRB1                 0          3          0          0          0          2
## KDM5B              390        442        379        405        398        489
## IL10                 8         16          7          2          0          4
## YOD1               244        255        237        213        319        261
## HHAT                40         27         18         16         45         36
## TRAF5              338        257        218        249        396        575
## NLRP3             1128        938        815        769        719        813
## LINC01250            0          0          0          1          0          0
## RPS7              6278       8199       7467       5947       7083       9750
## RSAD2              274        521       3346        942        309        753
## FOSL2             3633       3532       2437       3055       3268       3405
## REL               1055        824        749        875        955       1335
## TGFA               810        508        534        558        458        512
## DYSF              5989       5597       7120       7320       5753       4136
## HK2               1557       1155       1005        914       1152       1082
## CD8A              1283       1085       1205        422       1723       1293
## CD8B               537        490        506        157        819        590
## EIF5B              447        463        438        435        541        855
## IL1R1              232        334        203        306        222        222
## RGPD6               70         77         68         87         82        150
## IL1A                 0          1          0          0          2          0
## IL1B              1583        980        427        791       3503       2764
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             3275       2409       3311       3738       3015       2418
## NMI               2046       2070       2170       1420       1574       1799
## TNFAIP6            467        348        651        610        493        279
## IFIH1              421        414        637        489        434        705
## SCN1A                0          0          0          0          0          0
## ABCB11               2          0          0          1          0          0
## RBM45               48         54         50         45         81         80
## FRZB                 0          0          0          0          0          0
## TFPI                 3          4          2         22          5          3
## STAT1             4924       5330       4781       4727       4425       6131
## NABP1             1079        749        723        690        913        779
## SF3B1             4801       5728       3798       4135       4418       5203
## CASP10             313        415        252        337        302        616
## CD28               515        631        423        472        737       1032
## CTLA4               58        101         59         46         55         64
## ICOS               100        154        168        104        211        292
## NDUFS1             614        532        430        498        559        771
## CXCR2            22291      25091      25981      22691      30575      26602
## IRS1                78         50        140         86         49         76
## CCL20                3          2          2          0          1          4
## ATG16L1            262        296        216        226        284        430
## GPR35               85        133         52         75         65         93
## PDCD1               29         15         62         10         36         48
## PPARG                1          4          4          4          1          6
## RPL15            10179      14127      10853      10088      11431      15295
## EOMES              189         59        105         55        232        353
## CX3CR1            2331       1012       1590       1535       1617       3116
## ACKR2                0          0          2          0          0          1
## CCR2              1018       1018       1446        576        987       2901
## CCRL2               54         60         19         59         36         48
## TLR9                80         74         61         74         71        113
## ARHGEF3           1211        899        787        675       1058       1557
## ADAMTS9              0          0          0          1          0          0
## TMEM45A              3          3          0          7          0          5
## CD80                 6          4          2          0          3          7
## CD86               833        882        640        545        519       1236
## MIX23               22         28         22         26         31         55
## PLS1                14         14         19         27         21         28
## PTX3                65         62         46        144         21         46
## GOLIM4             101         87         78         64         83        140
## MYNN               328        350        284        292        278        400
## TNFSF10           3759       3652       4172       3934       3764       5525
## ADIPOQ               0          0          0          0          0          0
## SPON2              827        352        245        284        498        436
## S100P             2520       4618        256       3152       3181       2424
## WDR1              6381       6202       5572       6120       5895       6508
## CD38               365        161         61        242        112        338
## PPARGC1A             2          9          3          0          4          8
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          2          0          0          0
## CXCL8            64456      44699       4836      30523      16670      12954
## CXCL2               41         59          2          8          1          2
## AREG                19         94        116          6         11          6
## CXCL10              17         15         19         78         16         68
## CXCL13               0          0          4          0          1          0
## SPP1                34         80         11        192         24         79
## HERC6              181        177        366        204        178        245
## NFKB1             1050       1045       1064        890       1336       1503
## SEC24B             472        427        319        403        484        615
## EGF                 20         22          8        168         17         13
## IL2                  0          2          0          0          1          0
## IL21                 2          3          1          0          1          4
## IL21-AS1             1          1          1          1          3          4
## SLC7A11             22         14         11          8         13         14
## IL15                72         76         74         63         65        122
## EDNRA                0          0          0          0          0          0
## TLR2              5139       5358       6952       4612       4803       4470
## FGB                  0          0          0          0          1          0
## DDX60              321        294        906        456        341        671
## SPCS3             2082       2126       1680       1665       2339       2773
## TLR3                11          3          5          3         14         24
## OSMR                27         27         22         24         28         33
## GZMK               574        233        459        221        753        845
## GZMA              1162        563        707        426       1157       1338
## ANKRD55             73        144         63        155         64        124
## CENPK               18        108         13         28         20         30
## CAST              2772       2617       2767       2166       2898       2953
## ERAP1             1268       1193       1113       1254       2099       2043
## ERAP2              154       1474       1120        147       1496       2013
## TNFAIP8           1221       1350       1256       1231       1496       2242
## CSF2                 2          0          0          0          0          1
## IL5                  0          0          0          0          0          0
## IL13                 0          0          0          0          1          1
## IL4                  6         15          2          2          6         16
## CD14             11945      10171       8801      12641       8644       8509
## CSNK1A1           1626       1872       1482       1714       1766       2635
## PPARGC1B           132        114         81         83         91        157
## TNIP1             5094       4361       5399       5252       4955       4174
## ATOX1              177        199        140        161        128        183
## FAXDC2             120        152         97        368        140        140
## IL12B                0          0          0          2          1          0
## MIR146A              0          1          0          0          0          0
## PDLIM7            2205       2291       1917       1814       1699       1008
## SERPINB1          5456       5821       6545       5004       4673       3922
## SSR1              2267       2386       1927       1953       2181       2893
## CD83               653        293        149        557        267        221
## SOX4               150        171         64        112         57        168
## CMAHP               88         90         68         67         53        130
## HLA-A            45637      39900      46947      41110      40049      41793
## HLA-C            54714     102715      59177      86335      70731      51502
## HLA-B            76295     113315      73201      84654      82750      67320
## MICA               216        138        125        123        120        209
## LTA                 49         67         43         68         89        114
## TNF                194        328         71        346        214        216
## HLA-DRB1          6070       2769       2068       2061       2934       4349
## HLA-DQB1          2995        212        279       1625        476        501
## PPARD              277        283        275        275        336        501
## CCND3             3605       5555       5068       3966       3477       3880
## VEGFA              172        205         76        197         75        155
## RUNX2              408        494        373        364        456        549
## IL17A                0          0          0          0          0          0
## IL17F                0          0          0          0          0          0
## PRDM1              462        361        993        306        583        900
## ATG5               381        437        335        311        383        488
## TRAF3IP2           143        168        169        186        143        210
## NCOA7              303        352        364        407        449        609
## SGK1              5419       4803       1717       3373       2360       4748
## IFNGR1            4165       4215       4746       3472       3300       4200
## TNFAIP3           2598       3060       2945       1464       1362       1193
## SOD2             47597      49172      39547      48430      47688      36978
## LPAL2               25         21         10          5         16         29
## PLG                  1          1          1          0          0          0
## CCR6                74         41         95         40         90        337
## RAC1              3254       3220       2835       2487       2474       3097
## ZNF316             747        687        671        509        794        554
## AHR                726       1333       1281        465        711        906
## IL6                  1          0          2          0          1          2
## TOMM7             1788       1821       1539       1880       1851       2625
## CYCS               620        523        391        353        413        732
## AQP1                 4          4          3          7          5          2
## NT5C3A             689        625        640        736        658        640
## EGFR                 0          0          0          0          0          0
## CD36              2565       3031       2378       1701       1909       3686
## SAMD9             1975       1890       2688       1890       1919       2285
## SERPINE1             8         11          0         18          5          7
## CUX1              1552       1542       1219       1411       1206       1499
## PSMC2              343        375        336        266        362        605
## NAMPT            70200      53968      53012      51494      46224      35985
## HYAL4                0          0          1          0          0          0
## LEP                 14          1         10         13          1          5
## CALD1                5          3          4         89          2         10
## BRAF               651        625        486        694        608        677
## EZH2                67         59         48         46         50         79
## DNAJB6            1628       1535       1184       1477       1482       1641
## CSMD1                1         17          0          0          0          1
## CTSB              6947       5734       4670       4930       4444       8105
## EGR3               962        903       1173        685       1537        414
## TNFRSF10A          129        165         98        169        218        239
## BNIP3L            2533       2866       2039       2303       2326       2445
## DUSP4               21        101         28         14          2          8
## NRG1               111        103        144         29         55         39
## RPL7              7091       9529       7287       7790       8673      11245
## IL7                  6         12         14         11         14         22
## GEM                  1          1          0          0          1          2
## MYC                542        747        997        661        972       1371
## GPT                  2          1          3          0          1          3
## JAK2              1236       1039        877       1083       1171       1413
## CD274              180        165        293        157        340        287
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              1          1          1          0          1          0
## TTC39B              87        178         88        148        177        212
## IFNA1                0          0          0          0          0          0
## TEK                  8         16          7         14          7         11
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              182        240        143        152        197        302
## ANXA1             4931       8379       7412       5343       5648       5509
## ERP44             1478       1265       1038       1073       1215       1352
## ZNF483              18         28         22         22         41         39
## TNFSF15             16          1          3         11          7          9
## TLR4              8853       8700       8067       5289       6517       6853
## PTGS1              498        586        396       1295        440        724
## HSPA5             6432       5821       4627       3533       6900       4262
## FNBP1             3389       3409       3144       3363       3631       4377
## CARD9              189        258        140        107        125        166
## TRAF2              128        116        104        120        159        177
## CLIC3              128         72         78         56         75         80
## IL2RA               45        114        168         81        156        127
## GATA3              207        247        254        229        441        439
## VIM              13506      19826      14222      14235      14010      13498
## CREM               152        191        145        167        125        147
## DKK1                 0          0          0          1          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              912        882        688        823        798       1205
## PRF1              3345       1846       1476       1453       2471       3594
## ZMIZ1             1944       1910       1498       1974       1829       2091
## IFIT3             3564       4483      10262       4897       2796       4472
## TALDO1           11621      11012       9108       9013       8819       7495
## IGF2                 0          0          0          0          0          0
## INS-IGF2             0          0          0          0          0          0
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1274       1430       1213       1172       1400       1594
## TRIM22            2525       2954       3667       2091       2462       3923
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          0          0          0          0
## SLC1A2               1          0          0          0          1          2
## FOSL1               33         67         22         31         14          7
## CCND1               13          5          4          5         11         14
## JRKL                82         47         52         78        111        172
## MMP7                 0          0          0          1          0          0
## MMP1                 2          0          1          8          2          3
## MMP3                 0          0          0          0          0          0
## CASP1             3650       3558       3367       2047       2859       3450
## DLAT               199        164        158        145        202        277
## IL18                98        122         88         60         59        125
## CD3E              2345       2660       2450       2590       3752       3920
## MCAM               220        316        198        258        218        247
## WNK1              3678       3471       2964       4040       4002       4298
## TNFRSF1A          4743       4208       4505       4385       5009       5088
## GAPDH            20434      22103      21844      16544      15698      17327
## CD4               3926       3716       2761       4285       3935       5377
## SLC2A3           16273       9685       8282      13073       9638       4980
## CLEC4D             625        612        561        786        379        297
## KLRB1              846        345        466        312        670       1376
## CD69              2195       1731        837        485        482        356
## CLEC2B            2088       1773       1674       1377       1647       1769
## OLR1                10         40         14        288          7          4
## ABCD2              133        138        155        139        297        271
## LRRK2             9174       8987       7176       8839       8122       8193
## VDR                488        353        497        503        443        463
## TMBIM6           14743      15309      11131      12210      12872      14245
## PFDN5             2884       3970       3092       2632       2709       3700
## SP7                  0          0          0          0          0          0
## MUCL1                0          0          0          0          0          0
## CD63              3120       4051       2791       3068       2399       2465
## SUOX              1252       1075        859       1164       1009       1205
## RPS26              699        817        639        550       5944       6687
## RPL41             5777       7632       6599       5687       6566       7854
## IL23A               24         39         26         22         39         63
## DDIT3              779        604        325        479        359        304
## IFNG                31         26          1          7         12          5
## IL22                 1          0          0          0          0          0
## LYZ              78270      74485      48717      67601      50568      81466
## CAPS2                2          2          2          6          3          9
## SYT1                 1          0          8          2          0          4
## BTG1             10093      12139       6425       6992       6979       8575
## HCAR3             4667       3533       3637       3313       5167       3896
## GJB2                 0          0          0          0          0          2
## GJB6                13          5          4         33          3         13
## TNFSF11              1          2          6          1          1          0
## TPT1             41646      58783      47547      44091      47413      56172
## LMO7                51         74         45         98         89        120
## TNFSF13B          2507       1670       1966       1994       1997       2028
## LAMP1             3377       3017       2544       2817       2658       2653
## PSME2             1327       1351        958       1064       1038       1512
## GZMB               797        726        565        366        728        959
## RPL36AL           2168       2391       2004       1860       1833       2423
## PYGL              9179       7549       6791       6544       6842       4297
## HIF1A             2045       2325       1843       2285       1874       2020
## FOS              29005      58594       7754      14729      22770      20656
## JDP2               736       1071       1504        656        549        598
## NOXRED1             10         12          5          5          9          6
## SERPINA1         24243      22770      27192      29531      21123      23439
## CDC42BPB           192        206        178        205        197        292
## PLA2G4D              0          0          0          0          0          0
## TRIM69              18         17         23         11         24         12
## SLC51B               0          1          0          0          0          0
## SMAD3              551        465        530        401        674        810
## CYP1A1               2          3          0          2          1          2
## AKAP13            3891       4089       4082       3711       4212       5310
## MEFV              3226       3497       2514       3545       2855       3608
## SOCS1               51         82        124         25         42         38
## ATXN2L            1950       1631       1347       1547       1754       1901
## CD19               171         27        123         60         81        215
## ITGAL             6455       5394       4157       4604       6116       6577
## ITGAM             6213       5901       5748       5887       5140       4601
## ITGAX             7955       6155       5588       5290       5220       5289
## DNAJA2             743        730        636        621        727        984
## SIAH1              115        126        105        127        118        193
## ADCY7             2685       2299       2128       2065       2457       3318
## NOD2               488       1593        806        791        960       1186
## CMTM2             3077       2713       2736       2444       2054       1860
## SF3B3              950        847        751        801       1137       1355
## PSMD7              690        719        588        592        650        816
## WWOX                29         49         22         51         35         57
## MAF                456        452        421        263        582        856
## SLC7A5             195        198        221        230        247        155
## CXCL16            1894       2485       2337       1698       1519       1287
## XAF1               806        782       1744        956        580       1392
## CD68              4102       4443       3489       3254       2399       4813
## PER1               376        892       1712        331        262        347
## NOS2                 1          0          0          0          1          0
## TRAF4               76         99         40         53         60        149
## CCL2                29          6          5         11         32         33
## CCL5              3414       2038       2430       2483       3762       3026
## CCL3               617        389         25        220        196        206
## CCR7               587        888        978       1071       1182       2085
## STAT3             5877       5646       5020       5651       5293       5788
## SOST                 0          0          0          0          0          0
## ITGA2B             241        270        121       4138        214        312
## EFCAB13             24         20         16         11         15         16
## NPEPPS            1168       1071        847       1038       1019       1299
## TBX21              472        204        214        200        342        463
## COL1A1               0          2          0          1          0          0
## MRPS23             144        167        159        151        175        278
## MIR21                7          9          3          9          5          3
## RPS6KB1            372        330        296        355        387        560
## ACE                 15         31         61         18         80         57
## ERN1              1095       1047       1039        805       1359       1201
## PRTN3                0         46         16         89          6         10
## PLIN5              135        163        119        205        144         80
## RETN                35        152        127        247         40         48
## CCL25                0          2          0          0          0          0
## ICAM1             1733       2100       1657       1814       2079       1155
## TYK2              2112       2265       1727       1810       1771       2451
## SMARCA4            677        611        601        610        662        838
## ACP5               213        240        338        229        312        342
## JUNB             37533      39455      10048      23534      27414       9625
## CYP4F22             40         11         11         25         21         36
## JAK3              2447       2055       2226       2075       2489       2102
## JUND              5250       6935       3253       3213       4325       1956
## CEBPA              955        815        714        759        809        908
## CEBPG              310        309        218        211        271        479
## ACP7                 1          0          0          0          1          0
## ZFP36            31481      33510       6280      14608      16326      14367
## TGFB1             5394       5221       4750       4649       5307       4210
## RPS19             7135       9601       9149       7376       9436      11233
## PSG2                 0          0          0          0          0          0
## FUT2                 3          2          1          2          6          8
## NKG7              4006       2398       2285       1858       3725       3405
## ZNF415               6          3          4         10         14         12
## LILRB2            4697       4875       3970       4173       3338       4383
## LILRA5            2850       3762       3151       4193       2580       2512
## KIR3DL1             95         98          8         40         91         76
## KIR3DL2             54         35         41         33         63         54
## SMOX                81         72         59        186         85         69
## BMP2                12          9          7         11         10          4
## GINS1                9          6          5          9          6         15
## PLCG1              653        855        734        687       1127       1482
## YWHAB             5993       6001       5018       5632       5343       6621
## PI3               1306       1272       1799       3039       3401        720
## MMP9              2773       2436       2468       6210       2567       1362
## CD40               165         63        142        147        164        244
## PFDN4               44         42         31         38         45         59
## BMP7                 0          0          0          0          0          0
## RPS21             3029       4703       4229       3666       4405       5119
## MX1               1169       1674       3607       2001        556       2352
## PFKL              1215       1176       1022        923       1073       1406
## IL17RA            6312       6120       6473       6948       5746       7043
## UBE2L3            1030       1099        947       1063       1004       1298
## TPST2             1595       1230       1304       1050       1272       1147
## XBP1              1193       1072        976        652       1142       1618
## UQCR10             513        630        563        472        454        616
## SEC14L2             25         45         18         36         27         38
## APOL6             1501       1662       1787       1307       1785       2929
## APOL1              681        647        638       1204        740        762
## TYMP              3633       4322       5462       3419       2641       2308
## BEND2               26         35         22         26         31         18
## PHEX                 3         14          3          2          6         20
## TIMP1             1976       1367       1984       1730       1340       1165
## FOXP3               44         69         60         75         78         88
## MSN              26737      25942      19898      22455      21701      21316
## PGK1              8779       9626       8053       7253       7134       7506
## LAMP2             7639       7141       6019       7065       5955       5740
## CD40LG             133        138        162        152        266        378
## IRAK1             1461       1676       1189        976       1123       1438
## COX2             46111      36569      39269      38861      43491      37933
##             GSM3308509 GSM3308510 GSM3308511 GSM3308512 GSM3308513 GSM3308514
## TNFRSF9             79         50        189         98         96        127
## ENO1              7726       5901       3601       5810       6053       6072
## PIK3CD            4237       4667      12177       7057       5071       5979
## PGD               4941       7177       6102       3736       4579       6765
## MTHFR              347        325        369        460        356        407
## TNFRSF1B         14716      13765      14498      11567      13222      14211
## PINK1              478        703       1192        681        688       1016
## IFNLR1              20         51         48         83         29         56
## RUNX3             3483       2773       1709       3804       3462       4262
## SH3BGRL3         11079       9299       8466       8954      10673      10699
## CD52              4826       2696       2051       6038       4392       4561
## IFI6              1114       2881        577       1177        712        507
## ZC3H12A            765        368        437        382        487        443
## UTP11               80         50        115        167        102         87
## JUN               8126       2322        436       1404        820       9700
## KANK4                0          0          0          0          0          1
## EFCAB7              17         12         28         54         25         27
## IL23R                4          4          3          8          0          3
## ADGRL2               0          0          1          0          0          0
## GBP3               177        152        350        410        145        204
## GBP1               545       1655       1231       1184        487        525
## GBP5              1742       4456       3146       2378       1347       1100
## TGFBR3             640        446        377        941        629        929
## VCAM1                2         12          1          1          0          0
## PTPN22             318        341        402        574        256        438
## CD160               71         23         68        188         94        127
## FCGR1A             504        958        549        417        258        208
## MCL1             20167      39573      39390      21874      15751      17556
## CTSK                93         75         27         52         30         47
## RORC                28         30         79        100         64         60
## S100A9          168707     167363     145851      89157      79820     102411
## S100A12           5365       6602       4211       2221       2409       3652
## S100A8           66068      61366      60930      33972      29644      42066
## IL6R              2757       3270       8768       4031       3277       3603
## RIT1              1345       1653       1823       1220        991       1331
## BGLAP                7          3          5          8          8          5
## IFI16             1511       2451       5020       3304       1623       2066
## AIM2                56        159        289        179         54         75
## CRP                  0          0          0          0          0          0
## FCGR2A            8446       8596      26020      12843       8545       8853
## HSPA6             1366       1351       4992       2975       1377       1584
## FCGR3A           10414      17793      25094      15185      14826      14445
## SELL             18691      42106      45915      30100      24555      38389
## GLUL             15075      16800      22191      11400      10539      13182
## PTGS2             2983       1667      19403      12321       1611       4944
## CRB1                 1          1          4          2          2          0
## KDM5B              361        470        810        367        301        351
## IL10                19         29          0          1          2          3
## YOD1               321        652        342        206        251        211
## HHAT                24         26         24         45         25         40
## TRAF5              292        232        401        524        257        344
## NLRP3              685        879        433        476        880        504
## LINC01250            0          0          0          0          0          1
## RPS7              9291       6418       4426      11622       8103       7372
## RSAD2              478       1399        274        584        172        145
## FOSL2             3098       4820       5232       2080       3316       2829
## REL               1013        928       1478       1019        747        965
## TGFA               242        345       1310        412        337        539
## DYSF              3175       6202       8381       2999       2877       3896
## HK2               1006       1361       1754        934        528       1042
## CD8A              1432       1316        590       2134        753       3845
## CD8B               537        487        352       1015        361       1623
## EIF5B              375        253        372        733        345        463
## IL1R1              211        624        529        222        151        206
## RGPD6               94         51        101        126         62         54
## IL1A                 0          0          1          0          0          0
## IL1B               567        125       2159       1498        179        539
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             2522       1618       2951       2110       1528       1546
## NMI               1174       1656       1763       1675       1044       1330
## TNFAIP6            202        494        664        596        107        487
## IFIH1              258        348        385        506        269        298
## SCN1A                0          0          0          0          0          0
## ABCB11               0          1          1          0          0          1
## RBM45               62         40         53         80         44         48
## FRZB                 0          0          0          0          0          0
## TFPI                 3          6          9          5          4          8
## STAT1             2313       4948       5435       4236       2688       2862
## NABP1              525        738       1535        652        353        515
## SF3B1             4625       5058       5640       4963       3871       3867
## CASP10             325        315        386        419        301        259
## CD28               795        365        427        817        500        390
## CTLA4              132         93         37         87         90         69
## ICOS               203         68        131        216        152        107
## NDUFS1             405        409        589        657        462        476
## CXCR2             8207      12434      44849      19140      15068      14241
## IRS1                55         25         53         83         67         55
## CCL20                1          2          0          4          2          4
## ATG16L1            313        315        287        389        301        288
## GPR35              159        106         58         78        173         86
## PDCD1               23         46         21         68         24         54
## PPARG                4          2          3          3          3          1
## RPL15            14182      11033       7417      15632      13941      12001
## EOMES               46         39        135        259         33        194
## CX3CR1             336        132       1788       2250       1060       1123
## ACKR2                2          0          2          1          0          1
## CCR2               590        391       1098        939        496        416
## CCRL2               39         27         48         37         41         29
## TLR9                50         38        157         84         46         55
## ARHGEF3           1037        775        798       1227       1027       1040
## ADAMTS9              0          0          0          0          0          0
## TMEM45A              0          9          2          2          2          5
## CD80                 9          7          3          7          2          2
## CD86              1049        766        436        799        918        742
## MIX23               24         20         32         46         20         17
## PLS1                12         15         19         31         13         15
## PTX3                92         80         29         29         45         64
## GOLIM4              60         59         78        100        101         78
## MYNN               305        367        346        384        253        308
## TNFSF10           1481       1641       6207       3941       1642       2078
## ADIPOQ               0          0          0          0          0          0
## SPON2              332        322        585        627       1048        593
## S100P             1891       7214        347       1342       1475       1968
## WDR1              4619       4878       6362       5711       5331       6347
## CD38               171         94        304        267        325        335
## PPARGC1A             0          4         10          3          0          3
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          0          0          0          0
## CXCL8            47923      11270      18237      29355       8745      32455
## CXCL2               38         12          2         10          3         10
## AREG                96        731          7          6         48         37
## CXCL10               4          8         15         20          4         16
## CXCL13               0          0          0          0          1          0
## SPP1                21         64         93         65         47         63
## HERC6              128        220        173        274        133        157
## NFKB1             1053        708       1245       1053        679        832
## SEC24B             404        451        665        502        368        394
## EGF                 18         10         18         33         74         44
## IL2                  0          1          0          0          1          1
## IL21                 0          1          1          3          1          0
## IL21-AS1             1          0          2          1          1          0
## SLC7A11             18         22         29         18          5          5
## IL15                86         56         55         91         81         69
## EDNRA                0          0          1          0          0          0
## TLR2              3404       6047       9238       3143       2606       2198
## FGB                  0          0          0          0          0          0
## DDX60              241        531        368        465        238        230
## SPCS3             1854       1352       2072       2457       1576       1751
## TLR3                 4          4         15         27         13         17
## OSMR                27         41         61         20         33         24
## GZMK               400        412         60        583        243        830
## GZMA               818        440        695       1604        919       1535
## ANKRD55             63        105         55         87         79         52
## CENPK               27         65         16         24         75         62
## CAST              2359       1973       2653       3110       3684       2374
## ERAP1             1551        971       1222       1916       1885       1927
## ERAP2             1260        197       1001       1816       1272       1391
## TNFAIP8           1175        943       1426       2100       1068       1139
## CSF2                 0          0          1          0          0          1
## IL5                  0          0          0          0          0          0
## IL13                 2          0          0          0          0          0
## IL4                  0          1          4          4          7          8
## CD14             11430       5906       6420       5936       6090       8437
## CSNK1A1           1238       1277       2466       2087       1188       1486
## PPARGC1B           122         96         60         82        155         94
## TNIP1             4628       4481       4501       4796       3690       5290
## ATOX1              169        184        148        192        212        162
## FAXDC2             140         97        156        168        232        167
## IL12B                1          1          1          0          0          0
## MIR146A              0          0          0          0          0          0
## PDLIM7            1533       1926       2388       1599       1472       1624
## SERPINB1          4038       4431       5807       4224       3582       4679
## SSR1              2128       1830       2170       2651       1909       1876
## CD83               472        176        146        361        388        419
## SOX4               255        256         88        113        223        227
## CMAHP               67         58         86        122         85         82
## HLA-A            41885      38892      39335      36074      41148      38862
## HLA-C            78605      83189      79299      48174      72610      70589
## HLA-B            96574     103762     118220      81270      83117      93884
## MICA               101         89        160        170        109        109
## LTA                 40         20         47         79         41         64
## TNF                351         70        183        171        233        219
## HLA-DRB1          3765       3727       2893       5133       4026       2670
## HLA-DQB1          3012        893       2141       1393        398        326
## PPARD              291        297        307        393        310        266
## CCND3             3472       7169       4450       3897       4150       4808
## VEGFA              226        201        140        128        223        131
## RUNX2              453        673        672        504        379        585
## IL17A                0          0          0          1          0          0
## IL17F                0          0          0          0          0          0
## PRDM1              455        936       1118        578        397        558
## ATG5               403        334        366        470        403        393
## TRAF3IP2           232        163        166        237        175        139
## NCOA7              319        343        335        555        285        275
## SGK1              4607       1662       6125       3342       1695       2178
## IFNGR1            2355       4080       5766       3163       2462       2678
## TNFAIP3           4854       6970        956       1299       3108       3290
## SOD2             27061      35668      63236      31867      32016      33848
## LPAL2               17         12         20         14         12         21
## PLG                  1          0          0          0          0          0
## CCR6                92        105        245        187         62         81
## RAC1              2752       1883       3880       2570       2912       2806
## ZNF316             665        539        586        811        751        721
## AHR               1130       2366        434        776        720        662
## IL6                  3          3          3          1          0          4
## TOMM7             2352       1456        961       2508       1564       1971
## CYCS               490        392        320        686        486        541
## AQP1                 1          1          2          0          6          1
## NT5C3A             519        630        742        671        611        667
## EGFR                 0          0          0          0          0          0
## CD36              3474       1377       1079       2101       2456       1849
## SAMD9              904       1698       2960       2173        971       1202
## SERPINE1             8          3         14         13         17         10
## CUX1              1426       1708       1270       1023       1470       1474
## PSMC2              340        262        309        475        312        354
## NAMPT            47494      79673      70410      35939      31993      39655
## HYAL4                1          0          0          1          0          0
## LEP                  1          3          8          3         20          1
## CALD1                7          2         11         18         15         23
## BRAF               471        653        841        637        432        656
## EZH2                52         26         75         71         53         53
## DNAJB6            1352       1339       1894       1491       1488       1458
## CSMD1                6          1          0          3          5          3
## CTSB              6064       5996       3966       6330       7201       5024
## EGR3               384        439        661       1046        213        347
## TNFRSF10A          155        131        121        167        120        106
## BNIP3L            1958       2510       2352       2355       1846       2109
## DUSP4               98         45         23         16         90         40
## NRG1               170         27        119        162         76         94
## RPL7             11315       7226       5219      11698       9414       8413
## IL7                  5          7         20         27          7         10
## GEM                  0          0          1          1          1          0
## MYC                779        672        580       1004        580        411
## GPT                  2          2          2          1          3          5
## JAK2               744       1209       1078        960        680        922
## CD274              119         96        257        234         73         80
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              2          1          0          2          9          0
## TTC39B             180        136        161        220        176        155
## IFNA1                0          0          0          0          0          0
## TEK                  0         11         22         11         42          3
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              185        170        117        285        206        195
## ANXA1             7603       8304       3871       5225       6695       5353
## ERP44             1195       1223       1137       1306       1038       1161
## ZNF483              38         19         31         47         27         25
## TNFSF15              4          2          3          6          3          0
## TLR4              3322       7666       8897       6213       2914       5616
## PTGS1              787        407        756        565       1313        901
## HSPA5             4185       3462       4609       4466       3962       5051
## FNBP1             2889       2978       3828       3889       3229       3486
## CARD9              174        132        116        149        186        172
## TRAF2               96        104        121        165        104        124
## CLIC3               67         53        108        164        233        144
## IL2RA              121        140        102        108        101        102
## GATA3              218        135        202        514        308        311
## VIM              24562      13843      13366      13031      13995      14497
## CREM               222        226        121        147        166        124
## DKK1                 0          0          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              950        948        974       1027        738        677
## PRF1              1607       1322       2966       4290       2849       3265
## ZMIZ1             1705       1691       2917       1782       2304       2016
## IFIT3             2146       5781       3777       3510       1570       1191
## TALDO1            7856      10071      11830       8116       7931       8004
## IGF2                 0          0          0          0          1          0
## INS-IGF2             0          0          0          0          1          0
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1118       1056       1489       1340       1228       1327
## TRIM22            1408       4663       3323       2504       1447       1591
## PTH                  0          0          0          0          0          0
## SAA1                 0          1          0          0          0          0
## SLC1A2               1          2          1          0          1          0
## FOSL1               64        107          8         22         22         10
## CCND1                3          5          6          4          6          7
## JRKL                36         29        121        151         66         68
## MMP7                 0          0          0          1          0          0
## MMP1                 0          0          2          2          0          2
## MMP3                 0          0          0          0          0          0
## CASP1             2228       3115       2739       2707       2273       2123
## DLAT               102         85        133        271        171        197
## IL18                96        113         57         90         86         95
## CD3E              2584       1796       1419       4962       2554       3050
## MCAM               212        240        308        206        189        223
## WNK1              2517       2625       5055       3256       2725       3621
## TNFRSF1A          2159       3109       7155       3754       3083       2699
## GAPDH            23703      21837      11010      16716      17244      15139
## CD4               3921       2116       1678       4326       4431       2985
## SLC2A3            9679       8485      11856       5695       5399       7605
## CLEC4D             299        957        761        262        263        574
## KLRB1             1027        701        478       1071        926        707
## CD69              1738       1449        172        595        999       1450
## CLEC2B            1332       1491       1909       2073       1253       1144
## OLR1                 9         21         17         12          3         20
## ABCD2              173        103        143        255        137        118
## LRRK2             3946       8913      18384       6850       4533       5475
## VDR                398        375        803        377        284        356
## TMBIM6            9634      10434      14530      13996      10965      12073
## PFDN5             4056       2987       1882       3913       3262       2969
## SP7                  0          0          0          1          0          0
## MUCL1                0          0          0          0          0          0
## CD63              3075       2701       2684       2319       2519       2743
## SUOX               722        803       1438       1127        921       1094
## RPS26              819       2861       1898        890       3324        721
## RPL41             7314       5549       4130       9414       6963       5979
## IL23A               61         31         32         63         33         23
## DDIT3              562        662        726        418        458        596
## IFNG                47         15          4         15          4         90
## IL22                 1          0          0          1          1          0
## LYZ             156200      37943      17349      94208     120265      44499
## CAPS2                5          4          4          2          4          6
## SYT1                 3          6          1          5          1          1
## BTG1              9008      14371       7941       8594       6635      11648
## HCAR3             1642       1484       5580       2060        854       1380
## GJB2                 1         10          0          1          2          0
## GJB6                25        224          8          2         25          8
## TNFSF11              0          3          5          3          1          4
## TPT1             67120      44502      30937      67968      54084      44794
## LMO7                67         48         71        135         49         60
## TNFSF13B          1633       1862       2016       2312       1034       1367
## LAMP1             2478       2328       2633       2749       2460       2699
## PSME2             1269       1278        739       1257       1279       1137
## GZMB               603        396        697       1149       1285       1127
## RPL36AL           2605       1495       1434       1974       1892       2068
## PYGL              3956       6192       8061       3946       2752       5226
## HIF1A             2550       3900       2517       1654       2109       2190
## FOS              70837      52358      32230      16676       5344      70623
## JDP2               801       2795        787        621        717        714
## NOXRED1              9         10         24         11          1         10
## SERPINA1         24644      19582      28948      21861      21873      19919
## CDC42BPB           215        182        149        215        256        221
## PLA2G4D              0          0          0          0          0          0
## TRIM69              17         19         15         21          7         20
## SLC51B               0          0          0          0          0          0
## SMAD3              626        453        448        746        442        619
## CYP1A1               0          1          0          3          1          0
## AKAP13            3524       5837       5241       3614       3322       3132
## MEFV              1681       2265       6314       2436       2920       3208
## SOCS1               59        266         44         35         32         56
## ATXN2L            1360       1254       1269       1907       1594       1890
## CD19               100        131        184        229          0        112
## ITGAL             4216       3983       5196       5339       5457       5933
## ITGAM             4402       6130       5558       3543       4438       4294
## ITGAX             5099       6443       6948       3585       4024       4632
## DNAJA2             632        658        815        822        494        651
## SIAH1              149        141        201        121        104         93
## ADCY7             1621       1584       3008       2620       2948       2296
## NOD2               451        874        446       1109        830        629
## CMTM2             2095       3047       3068       1864       1876       1952
## SF3B3              614        459        594       1078        673        816
## PSMD7              845        688        579        781        679        646
## WWOX                64         44         23         44         41         25
## MAF                382        434        399        590        406        567
## SLC7A5             211        437        208        180        286        188
## CXCL16            1568       4069       1976       1331       1622       1858
## XAF1               643       1284        657       1025        714        475
## CD68              5627       4141       1897       2800       4946       3573
## PER1              1106       7359        249        334        754        601
## NOS2                 1          2          0          1          6          0
## TRAF4               93         74         84        136         90         95
## CCL2                 4          0          2         26          0          8
## CCL5              2665       2233       1610       5182       3016       6295
## CCL3               249         32        148        112         59        484
## CCR7               902        471       1017       1543        716        392
## STAT3             3184       4986       9352       4570       3403       4000
## SOST                 0          0          0          0          0          0
## ITGA2B             271        131        484        417        784        600
## EFCAB13             21         17         25         22         26         20
## NPEPPS             682        883       1637        961        734        867
## TBX21              242        250        346        621        495        544
## COL1A1               1          0          0          0          0          0
## MRPS23             179         91        123        279        164        178
## MIR21                6         12          9          5          3          3
## RPS6KB1            316        343        417        473        306        341
## ACE                 22         38         26         87         44         46
## ERN1               878       2212       2260       1350        897       1429
## PRTN3               23         86          9          8          3         79
## PLIN5               68        142        207        101         55         99
## RETN               108         77         43         39         63        103
## CCL25                0          0          0          0          0          3
## ICAM1             1949       1673       1129       1171       1152       1642
## TYK2              1454       1898       3257       1935       1555       1772
## SMARCA4            533        451        456        866        703        715
## ACP5               288        243        169        460        297        210
## JUNB             42799      23043      23742      22345      11329      40255
## CYP4F22             13         37          6         17         65         85
## JAK3              1546       1596       2337       1981       1362       1532
## JUND              7373       6697       3898       4595       4910       7525
## CEBPA             1121        706        720        535        969        801
## CEBPG              292        179        253        373        278        239
## ACP7                 0          0          0          0          1          0
## ZFP36            37491      12781      25978      13303       6540      27311
## TGFB1             4664       4757       4024       5250       5585       5874
## RPS19            10203       7618       5065      12331       9760       9625
## PSG2                 0          0          0          0          0          0
## FUT2                 3          1          2          4          0          0
## NKG7              2682       2366       2014       5480       3850       5989
## ZNF415               0          1        256         14          7          1
## LILRB2            4948       4803       4560       3206       5412       4622
## LILRA5            2843       2136       2795       2209       2759       3542
## KIR3DL1            125         66         53         26         74         42
## KIR3DL2             37         52         27         32         47         71
## SMOX               127         87        101         82        240        116
## BMP2                 3         21          3          5          2         12
## GINS1               10          5         11         10          3          8
## PLCG1              721        542        668       1158        710        715
## YWHAB             4713       4120       5303       6646       4899       5751
## PI3               2709        279       1088        901        696        964
## MMP9              3284       5107       2913       1152       1744       3492
## CD40               122        103        144        239        145        125
## PFDN4               48         25         23         62         58         57
## BMP7                 0          0          0          0          0          0
## RPS21             4959       3386       2367       6581       4760       4049
## MX1                638       2183       1198       1027        599        593
## PFKL               919        937        763       1214       1374       1116
## IL17RA            4367       5813       9511       4509       4435       4529
## UBE2L3             819        790        909       1168        933       1028
## TPST2             1042        939       1062       1295       1320       1350
## XBP1               991        787        922       1347       1088        867
## UQCR10             495        415        390        633        599        471
## SEC14L2             45         29         13         48         24         23
## APOL6              855       1838       2183       1706       1016        848
## APOL1              362        547        771        535        668        398
## TYMP              3621       4136       3609       2939       2467       3548
## BEND2               24         10         66         44        103         95
## PHEX                 6          4         12         13         11          5
## TIMP1             1907       2379       1606       1016       2080       1383
## FOXP3               77         44         58         61         74         84
## MSN              20885      22709      25201      19608      22480      25266
## PGK1              7607       7916       6840       6675       6778       6914
## LAMP2             4684       6222       9673       5619       5474       6117
## CD40LG             133         95        154        380        166        125
## IRAK1             1591       1766       1151       1503       1611       1499
## COX2             60802      29386      15056      46987      59283      54615
##             GSM3308515 GSM3308516 GSM3308517 GSM3308518 GSM3308519 GSM3308520
## TNFRSF9            107         93        119         77         78        100
## ENO1              3292       6795       6136       6768       6746       6060
## PIK3CD            4957       7936       6970       7212       4280       6055
## PGD               2487       4480       4433       6070       4640       4228
## MTHFR              234        563        439        396        366        535
## TNFRSF1B          8044      12324      11735      15495      13051      10954
## PINK1              490        758        861        862        775        762
## IFNLR1              47         70         77         68         78         81
## RUNX3             1845       2913       4229       2512       6539       4391
## SH3BGRL3          5374       9044       9207      11429      13967      10463
## CD52              2628       5277       4042       5178       5992       3435
## IFI6               824       4523        851       6691        968       1778
## ZC3H12A            239        354        348        347       1423        239
## UTP11              106        241        157        178        122        157
## JUN                177        669       2578        736       2526        296
## KANK4                0          0          0          1          0          0
## EFCAB7              26         41         41         28         14         41
## IL23R                3          6         13          5          1          9
## ADGRL2               0          0          0          0          0          0
## GBP3               198        549         87        385         89        239
## GBP1               847       2223        809       3423        431       2179
## GBP5              2200       3789       1651       4595       1584       4785
## TGFBR3             427        477        940        468       1021       1056
## VCAM1                1          1          1          0          7          3
## PTPN22             425        573        631        541        375        634
## CD160               40         90        150        175        192        323
## FCGR1A             181        558        325        982        476        776
## MCL1             13948      27084      16716      22072      22346      22782
## CTSK                25         51         67         27         46         19
## RORC               177        144        269        159         35        117
## S100A9           49688      73813      73550     110677     131510      82837
## S100A12           1173       1278       1091       3391       3090       2199
## S100A8           18228      26371      26505      48372      48350      29092
## IL6R              3556       5349       3635       7202       3785       5777
## RIT1               638       1040       1045       1325       1462       1157
## BGLAP                5          7          8          6          6          5
## IFI16             2319       5275       3051       6031       1287       4672
## AIM2                72        198         65        367         45        207
## CRP                  0          0          0          0          0          0
## FCGR2A            6875      10967      10442      11716       7309      13387
## HSPA6             1376       2184       1792       3263        736       2065
## FCGR3A            9917      16987      14700      38299      12123      27122
## SELL             14775      32334      23640      39836      25701      27030
## GLUL              6999      11035      11733      14024      13102       9422
## PTGS2             9079      10174       5280       1938       1031      10868
## CRB1                 1          0          0          4          0          2
## KDM5B              330        476        430        594        412        502
## IL10                 1          2          0          6          1          1
## YOD1               145        207        229        198        288        169
## HHAT                20         41         32         41         45         36
## TRAF5              268        399        556        303        244        382
## NLRP3              444        853        494        824        828        690
## LINC01250            0          0          0          0          0          0
## RPS7              5505       8607       9598       8685      13987       9173
## RSAD2              511       3461        300       8197        228        831
## FOSL2             1948       2621       2704       2415       4237       2594
## REL                644        907        982       1007       1253       1255
## TGFA               372        429        588        565        279        449
## DYSF              1958       3309       2609       4123       2235       3848
## HK2                726        871        836       1151        650        953
## CD8A              1187       1894       3037       1105       2558       2325
## CD8B               539        899       1069        448       1146       1159
## EIF5B              418        775        715        850        408        644
## IL1R1              111        177        210        146        266        149
## RGPD6               74        108        104        109         66         98
## IL1A                 0          0          1          0          0          0
## IL1B              2099       2107       1202       1822        384       1331
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             1309       2929       2004       3912       3272       1953
## NMI                938       2101       1362       2217        818       1622
## TNFAIP6            152        280        242       1683        127       1460
## IFIH1              349       1026        398       1220        300        734
## SCN1A                0          0          0          0          0          0
## ABCB11               0          2          0          0          0          0
## RBM45               33         95         69         77         48         65
## FRZB                 0          0          0          2          0          0
## TFPI                 1          3          6          2          1          4
## STAT1             3077       6681       3009       8620       2154       6375
## NABP1              424        769        573        559        264        472
## SF3B1             2209       4743       4384       3294       4899       3745
## CASP10             322        657        362        557        280        450
## CD28               800       1143        712        980        434        559
## CTLA4               35         76         53         26         88         27
## ICOS               141        286        141        167        194        224
## NDUFS1             355        739        558        756        427        665
## CXCR2            13337      23761      16032      25115       9459      28680
## IRS1                46         98         93         33         66         80
## CCL20                3          0          0          6          8          1
## ATG16L1            242        377        374        281        340        265
## GPR35               76         80        112        109        141         97
## PDCD1               35         75         73         38         43        111
## PPARG                2          3          2          6          7          4
## RPL15             8435      14527      15203      13888      22464      15612
## EOMES              161        232        396        384        166        607
## CX3CR1            1960       3241       2049       4441        546       3590
## ACKR2                2          2          4          2          0          0
## CCR2              1277       2025       1099       2441        427       2427
## CCRL2               37         62         28        108         29         47
## TLR9                93        108         81        120         43         85
## ARHGEF3           1000       1474       1093       1488        872       1249
## ADAMTS9              0          0          0          0          0          0
## TMEM45A              0          2          4          1          0          0
## CD80                 0          6          5         10          3          9
## CD86               485       1218        831       1782       1011        930
## MIX23               28         48         43         39         27         29
## PLS1                17         30         28         17         18         16
## PTX3                14         23         21         53         99         30
## GOLIM4              65        141        109        131         87        112
## MYNN               210        329        343        340        461        337
## TNFSF10           2950       6194       2718       6678       1185       4026
## ADIPOQ               0          0          0          0          0          0
## SPON2              323        371        640        570        773        975
## S100P             1235       1969       1598       3444       2689         98
## WDR1              3842       6555       6096       6707       5108       6405
## CD38                86        295        270        321        278        296
## PPARGC1A            12          1          5          0          1          7
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          1          0          0          0
## CXCL8             6921      15955      24901       7046      27758      14849
## CXCL2                1          2          5          3          6          2
## AREG                 2          5          7          1        306          7
## CXCL10               6         61         22         83          4         60
## CXCL13               0          0          0          0          0          2
## SPP1                 8         46         52         31         84         15
## HERC6              153        493        260        569        105        255
## NFKB1              882       1491       1059       1331        766       1288
## SEC24B             356        597        490        636        415        538
## EGF                 19          9         17         20          6          5
## IL2                  0          1          0          0          0          0
## IL21                 0          1          1          0          0          2
## IL21-AS1             0          1          0          0          1          1
## SLC7A11              0         11          3          8          5         38
## IL15                62        121         97        127         50         89
## EDNRA                0          0          0          0          0          0
## TLR2              1897       4062       2746       4602       3412       7861
## FGB                  0          0          0          0          0          0
## DDX60              354       1290        455       1563        184        748
## SPCS3             1479       2586       2576       2393       2149       2481
## TLR3                24         19         19         18         15         20
## OSMR                16         20         18         15         28         22
## GZMK               200        454       1224        922        867        934
## GZMA               608        941       1811       1222       1621       2004
## ANKRD55             32        140         91         81         57         52
## CENPK               42         75        143         50         51        119
## CAST              1518       2865       2473       3307       3323       2520
## ERAP1              968       1891       1568       1950       2101       2386
## ERAP2              980       3290       1540        140        128        174
## TNFAIP8           1259       2075       1675       1901       1072       1824
## CSF2                 1          0          0          0          7          0
## IL5                  0          1          0          0          1          0
## IL13                 0          3          0          1          2          0
## IL4                  4         11          8          4          2          3
## CD14              4936       6919       6892       7135       8560       6072
## CSNK1A1           1565       2373       1831       2799       1163       2516
## PPARGC1B            48        141        108         92         84         73
## TNIP1             2300       3684       4158       4880       3927       4187
## ATOX1               96        204        178        266        211        166
## FAXDC2             111        156        140        142        107        114
## IL12B                0          3          0          1          0          0
## MIR146A              0          1          0          0          0          0
## PDLIM7             849       1309       1560       1469       1588        994
## SERPINB1          2486       4446       4072       4564       4429       4002
## SSR1              1377       2627       2396       2975       2497       2500
## CD83               111        360        338        191        831        111
## SOX4                71        123        162        195        225        138
## CMAHP               71         82        127         66         62         60
## HLA-A            25133      56281      48577      56711      43361      42062
## HLA-C            41572      54181      70195      82194      83095      61311
## HLA-B            53616     115903      97340     115083     113383     113862
## MICA                95        162        151        180        116        127
## LTA                 59        103         76         63         40         60
## TNF                211        270        159        246        417        116
## HLA-DRB1          1755       5061       5554       5847       3853       3315
## HLA-DQB1           482       1050       1420       1897        765       1009
## PPARD              246        402        329        378        317        327
## CCND3             2412       4759       4220       4047       5894       6586
## VEGFA               76        153        119        122        181        110
## RUNX2              480        581        567        513        549        517
## IL17A                1          0          0          1          0          0
## IL17F                0          0          0          0          1          0
## PRDM1              601        983        552        836        780       1198
## ATG5               276        583        457        497        502        482
## TRAF3IP2           146        243        238        206        191        163
## NCOA7              335        660        372        502        341        553
## SGK1              2460       3707       2863       1944       2128       4032
## IFNGR1            2259       3314       3188       4352       1887       4929
## TNFAIP3            769       1276        897       1353      12478       1452
## SOD2             19115      32084      34246      35588      38183      41788
## LPAL2               15         12         20          8         12          5
## PLG                  0          0          2          0          0          0
## CCR6               279        268        186        311        104        195
## RAC1              1930       3010       2669       2993       3321       3485
## ZNF316             424        657        851        376        625        451
## AHR                609       1039        780        959       1527        794
## IL6                  0          2          3          1          7          2
## TOMM7             1457       2549       1863       2329       2356       1832
## CYCS               396        754        600        636        660        665
## AQP1                 1          6          7          0          2          0
## NT5C3A             417        911        637       1240        522        626
## EGFR                 0          0          0          0          0          0
## CD36              1211       3342       1722       2659       2182       1996
## SAMD9             1192       3019       1601       2662        862       1811
## SERPINE1             9          7         11          6          4          8
## CUX1               681       1310       1188       1651       1663       1361
## PSMC2              354        644        419        684        350        505
## NAMPT            18755      30781      32113      36838      40776      41614
## HYAL4                0          0          0          0          0          0
## LEP                 15         30          4          6          5         13
## CALD1               16         11          8          7          5          8
## BRAF               405        636        689        548        606        627
## EZH2                42        115         53         64         51         65
## DNAJB6            1020       1627       1313       1368       1423       1741
## CSMD1                3          1          0          5          2         28
## CTSB              2983       6937       4154       8836       5991       4636
## EGR3               329        700        406         68        701        231
## TNFRSF10A          142        220        148        125         98        186
## BNIP3L            1234       2323       1932       2354       2277       2232
## DUSP4               16         47          7         14         39         20
## NRG1                48         22        156        136         41        110
## RPL7              6107      10445      11313      10057      14091      11047
## IL7                 11         23         16         18         11         15
## GEM                  3          3          2          4          1          0
## MYC                620       1359        868       1013        358        915
## GPT                  1          4          4          3          2          1
## JAK2               667       1374        910       1173        692        992
## CD274               76        203        142        570         81        289
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              0          1          1          0          0          1
## TTC39B             120        241        218        157        146        162
## IFNA1                0          0          0          0          0          0
## TEK                 10          5         13         10          7         24
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              164        323        266        279        295        243
## ANXA1             3505       9303       6782       7566      12015       5255
## ERP44              648       1415       1126       1458       1305       1223
## ZNF483              29         45         29         41         30         26
## TNFSF15             11         11          4         14          0          9
## TLR4              3669       6579       4853       6759       2948       7668
## PTGS1              430        555        745        458        458        406
## HSPA5             2331       4457       4064       3821       6322       4451
## FNBP1             2506       4078       4199       3497       3387       3983
## CARD9              142        246        174        204        138        146
## TRAF2              117        193        165        182        129        153
## CLIC3               96        148        148        139        209        263
## IL2RA              119        243         96        106         67        105
## GATA3              327        537        443        386        273        356
## VIM               7562      18381      12143      16609      21123      16310
## CREM                85        134        138        158        257        133
## DKK1                 0          0          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              697        966        845       1364        891        965
## PRF1              2413       2859       3311       4030       1780       5294
## ZMIZ1             1288       2264       1885       1868       2620       1967
## IFIT3             2698      12366       2601      17241       1422       5928
## TALDO1            4693       7860       8058       9015       9016       8102
## IGF2                 0          0          0          0          0          0
## INS-IGF2             0          0          0          0          0          0
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1              931       1397       1297       1270       1735       1351
## TRIM22            1907       5349       2262       5976       1292       3522
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          0          0          0          0
## SLC1A2               0          2          4          0          3          1
## FOSL1                1          7         13          4         51          4
## CCND1               12         10         13         11          5         12
## JRKL                80        118        122        132         49         98
## MMP7                 0          1          0          0          0          0
## MMP1                 0          0          0          0          0          0
## MMP3                 0          0          0          0          0          0
## CASP1             1791       3328       2684       4101       2035       2856
## DLAT               147        238        224        221        146        247
## IL18                58        110        107        105         96        102
## CD3E              2406       4035       3769       3216       3303       3870
## MCAM               179        245        262        397        273        245
## WNK1              2500       3684       3691       3802       2810       4651
## TNFRSF1A          2676       4680       3927       4733       2519       5198
## GAPDH             7681      12937      14733      17408      21586      13980
## CD4               2983       4895       3363       5895       3576       3308
## SLC2A3            3340       4428       5999       6947       6182       3933
## CLEC4D             232        285        240        540        251        295
## KLRB1              698        643       1815       1407       1657       1577
## CD69               206        425        630        180       2067        425
## CLEC2B             856       1717       1610       2101       1348       1461
## OLR1                12         12          4         19         89         10
## ABCD2              182        263        192        191        136        224
## LRRK2             4732       6946       5279       7629       5153       9184
## VDR                265        493        382        639        268        322
## TMBIM6            7780      14055      13236      14080      12692      14091
## PFDN5             1997       3518       3554       3545       5881       3622
## SP7                  0          0          0          0          0          0
## MUCL1                0          0          1          0          0          0
## CD63              1392       2325       2777       2977       4675       2655
## SUOX               683       1162       1192       1285        921       1165
## RPS26             4182       3865       4102       3828       1281        788
## RPL41             4599       7983       8110       8068      11463       8250
## IL23A               44         65         30         70         27         32
## DDIT3              167        270        430        303        417        217
## IFNG                 6         14         14         16         33         11
## IL22                 0          0          0          0          0          0
## LYZ              58532      49037      36533     130117      83424     113114
## CAPS2                1          6          9          5          9          7
## SYT1                 0          9          9          1          2          1
## BTG1              4843       7884       9023       9576      11369       9274
## HCAR3             1672       2070       2340       2464       1611       3100
## GJB2                 2          0          2          0          2          0
## GJB6                 3          7         10          5         16          1
## TNFSF11              4          5          3          1         17          9
## TPT1             33750      55354      53617      48754      73724      55682
## LMO7                77        110        110         82         47         94
## TNFSF13B          1135       2895       1803       3323       1667       2160
## LAMP1             1534       2726       2349       3034       2588       2378
## PSME2              757       1830       1262       1958       1381       1389
## GZMB               977        959       1134       1278       2132       1634
## RPL36AL           1184       2527       1746       2403       2810       2468
## PYGL              2395       3586       4245       3584       3023       3737
## HIF1A             1235       1829       1830       2999       3127       1701
## FOS              16149      36253      16014      40012       7301      15293
## JDP2               358        697        588        624        874        719
## NOXRED1              3         11         11          3          7          2
## SERPINA1          9683      18343      16343      24123      16675      19963
## CDC42BPB           115        306        221        191        236        202
## PLA2G4D              0          0          0          0          0          0
## TRIM69               7         37         10         17         15         17
## SLC51B               0          0          0          0          0          0
## SMAD3              510        721        814        791        741        678
## CYP1A1               1          1          0          0          2          1
## AKAP13            2789       4818       4074       5276       4556       5974
## MEFV              1933       2717       2886       2858       1825       3292
## SOCS1               27         65         35         99         66         53
## ATXN2L            1052       2032       1949       1270       1562       1438
## CD19                95        132        309        193        128        109
## ITGAL             3513       5031       5193       4801       5364       5473
## ITGAM             1844       3887       3752       4710       5173       4697
## ITGAX             1565       2563       4965       2960       4297       2786
## DNAJA2             528        886        742        913        513        878
## SIAH1              146        240        150        236        158        188
## ADCY7             1484       2981       2555       2085       2717       2438
## NOD2               296        911        629       1152        671       1358
## CMTM2             1044       1575       1952       2913       2173       2453
## SF3B3              712       1166       1058       1180        626       1181
## PSMD7              466        855        747        793        801        731
## WWOX                27         54         52         40         51         36
## MAF                476        753        556        461        445        442
## SLC7A5             149        223        254        210        402        237
## CXCL16             548       1348       1344       1731       1656       1685
## XAF1               599       2769        805       2161        422        817
## CD68              2015       4481       2971       6303       5223       3942
## PER1               130        325        276        202       1973        493
## NOS2                 1          1          3          1          5          0
## TRAF4               75        116        131        111        175        100
## CCL2                27        226         40         83         10         21
## CCL5              2412       2802       5426       2888       6637       7174
## CCL3                98        310        153        177        249        310
## CCR7              1089       2188        899       1808        564       1783
## STAT3             3299       5241       4489       5980       2916       5656
## SOST                 0          0          0          2          0          0
## ITGA2B             186        248        238        124        127        113
## EFCAB13             18         20         22         21         15          8
## NPEPPS             660       1144        993        850        602       1043
## TBX21              423        411        540        437        483        714
## COL1A1               0          0          0          0          1          0
## MRPS23             171        243        221        276        204        285
## MIR21                4          4          8          3          4          3
## RPS6KB1            298        461        433        349        341        460
## ACE                 45         67         49         36         30         31
## ERN1               715       1244       1693       1326       1309       1333
## PRTN3                2          3         23          7         69          4
## PLIN5               38         99        100         61         49         53
## RETN                25         77         32         96        235        334
## CCL25                0          0          0          0          2          0
## ICAM1              427        671        948       1150       2423        820
## TYK2              1251       2350       2340       1867       1147       1641
## SMARCA4            453        870        832        713        657        707
## ACP5               240        457        334        576        327        335
## JUNB             10577      22859      21500      17193      16066      10429
## CYP4F22             13         24         41         36         26         20
## JAK3              1125       1768       1904       1213        970       1081
## JUND              1919       4486       4129       2948       7141       2543
## CEBPA              503       1048        637       1336       1021        636
## CEBPG              295        499        315        503        283        406
## ACP7                 1          0          3          0          0          0
## ZFP36            11116      22499      10034      16005      13682      11789
## TGFB1             3038       5072       4842       5107       5168       4308
## RPS19             6440      10671      11139      10281      13830      10252
## PSG2                 0          0          0          0          0          0
## FUT2                 2          3          2          2          4          3
## NKG7              2359       2984       6015       3381       8003       6837
## ZNF415               5         15         14         10          3         18
## LILRB2            1978       4069       3526       4842       4594       2468
## LILRA5            1338       1576       2214       3931       1550       2127
## KIR3DL1             85         47        107         15        359         35
## KIR3DL2             58         63         73         30         96         33
## SMOX                48         75         94         53         59         35
## BMP2                 3          1          3          1          6         11
## GINS1                7         12          7         18          7          7
## PLCG1              737       1373       1164        668        499        911
## YWHAB             3670       6297       5411       6621       4998       5735
## PI3                544        955        608       1419       2372        811
## MMP9               739       1044        909       2691       1499        747
## CD40               107        169        233        234        189        160
## PFDN4               30         58         54         53         65         38
## BMP7                 0          0          0          0          0          0
## RPS21             3064       5154       5510       4765       7299       5306
## MX1               1109       4633        939       7442        659       2237
## PFKL               790       1706       1129       1124        927       1229
## IL17RA            3338       5915       4150       6080       3159       6565
## UBE2L3             726       1330       1177       1481       1051       1312
## TPST2              665       1255       1254        840       1395       1348
## XBP1              1110       1759       1186       1626       1459       1699
## UQCR10             396        604        653        755        719        634
## SEC14L2              7         21         20         10         28         16
## APOL6             1375       2529       1309       3651       1056       2901
## APOL1              320       1001        748       1150        422        619
## TYMP              2498       6194       2224       2984       2636       3008
## BEND2               24         21         24         25         11         18
## PHEX                 4         22          2         10         13         13
## TIMP1              723       1755       1239       2384       2754       1282
## FOXP3               78        144         59         87         40         67
## MSN              11949      20201      20114      22288      23987      24252
## PGK1              3813       6641       6215       6752       9258       6404
## LAMP2             3455       5559       5232       6886       6083       6493
## CD40LG             198        366        230        317         68        219
## IRAK1              814       1429       1590        982       2119       1189
## COX2             25819      60059      59276      44790      78004      54196
##             GSM3308521 GSM3308522 GSM3308523 GSM3308524 GSM3308525 GSM3308526
## TNFRSF9            156        146        134        168        106        121
## ENO1              6184       5960       7203       6737       6283       7027
## PIK3CD            6631       9047       4959       7145       5438       5688
## PGD               4884       5249       5133       4048       4326       4333
## MTHFR              397        383        411        478        440        505
## TNFRSF1B         18163      13045      11307      11246      14472      13965
## PINK1              784        938        725        778        822        715
## IFNLR1              43         70         49         88         93         66
## RUNX3             3492       2074       2087       5164       6669       5541
## SH3BGRL3         11438       8090      10297       9539      12040      10273
## CD52              3331       3970       5650       5752       6243       5275
## IFI6              2059        815       3127        607       2135        504
## ZC3H12A            471        355        907        500        748        597
## UTP11              107        163         86        154         74         87
## JUN               3811        984      14634       2095       8972       6964
## KANK4                0          0          0          0          0          1
## EFCAB7              24         35         14         31         24         18
## IL23R                4          5          0          3          0          4
## ADGRL2               0          0          0          0          0          0
## GBP3               136        205        302        370        192         66
## GBP1              1072        949       1337       1175       1511        495
## GBP5              3427       2101       3445       3374       6763       1452
## TGFBR3             679        470        220       1502       1972       1710
## VCAM1                2          0          0          9          1         17
## PTPN22             326        514        183        639        393        399
## CD160               87         81        105        289        176        195
## FCGR1A             755        385       1855        468       1191        610
## MCL1             19949      26431      14377      23528      19484      22229
## CTSK                59         25         48         41         72         45
## RORC                67        148         38         86         25         26
## S100A9           96845     118387     149710     103311      92239     100421
## S100A12           1877       3247       5526       3049       2181       3144
## S100A8           34686      49499      63535      39866      32019      36797
## IL6R              4835       7530       2463       4974       3390       4136
## RIT1              1262       1539        690       1297       1341       1255
## BGLAP                7          7         12         12          8          4
## IFI16             2854       4585       1452       3658       2107       1850
## AIM2               119        190        148        154        153         84
## CRP                  0          0          0          0          0          0
## FCGR2A           13317      18053       9643      12400       9875      10674
## HSPA6             1695       2670       1227       1875       1826        907
## FCGR3A           19521      22188      16305      16406      17265      14070
## SELL             37147      32804      35832      29897      31810      25486
## GLUL             17565      14215       8593      10779      14169      15823
## PTGS2             3976      20120      13124      18859       3719       5872
## CRB1                 1          1          0          1          2          1
## KDM5B              395        618        285        412        412        406
## IL10                 3          1          3          3          1          6
## YOD1               200        210         66        152        295        334
## HHAT                37         48         27         46         42         54
## TRAF5              291        372        175        569        295        315
## NLRP3              632        677        838        576        626        647
## LINC01250            0          0          0          0          0          0
## RPS7              8433       8679      10362      11562      10368       9774
## RSAD2              942        418        813        289        951        116
## FOSL2             3624       3925       2132       2632       4729       5178
## REL               1219       1486        441       1199       1014       1270
## TGFA               439        944        423        500        329        309
## DYSF              4487       6068       4126       3853       3790       3794
## HK2               1024       1641       1250       1045        750        964
## CD8A              1147       1735        968       4866       4475       2689
## CD8B               624        877        553       1755       1517       1051
## EIF5B              432        650        355        740        517        566
## IL1R1              252        270        124        175        171        221
## RGPD6               72        119         32        122         81         81
## IL1A                 1          0          1          0          0          0
## IL1B               267       4850       2608       1195        260        355
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             2744       2969       5471       1705       2706       2623
## NMI               1454       1745       1044       1387       1229        995
## TNFAIP6            647        663        381        642        513        444
## IFIH1              508        559        445        463        485        302
## SCN1A                0          0          0          0          0          0
## ABCB11               0          1          0          0          0          1
## RBM45               46         69         42         73         50         40
## FRZB                 0          0          0          2          0          0
## TFPI                 5          4          3          5          4          6
## STAT1             4660       3597       3809       3896       5384       2640
## NABP1              511        925        676        715        367        413
## SF3B1             5005       4428       2833       5143       4574       4491
## CASP10             256        476        313        350        226        317
## CD28               451        931        382        741        468        632
## CTLA4               69         38         24         62         85         85
## ICOS               131        247         96        263        134        181
## NDUFS1             491        654        345        690        459        452
## CXCR2            21418      33666       8513      20659      11731      16956
## IRS1                72         86         53        105         63         67
## CCL20                2          3          8          2          1          5
## ATG16L1            227        285        242        425        358        317
## GPR35               91         54         97         99        198         75
## PDCD1               31         75         31        127         21         30
## PPARG                1          2          6          8          2          1
## RPL15            13794      13160      13895      17102      16075      15288
## EOMES              132        206         96        525        266        229
## CX3CR1             839       2057       2047       3375        702        757
## ACKR2                0          4          0          2          0          2
## CCR2               577       2009       1471       1688        375        513
## CCRL2               29         47         41         32         42         40
## TLR9                51        122         31         87         49         37
## ARHGEF3            891       1044        743       1399       1275       1343
## ADAMTS9              0          0          0          0          0          0
## TMEM45A              7          0          0          8          2          1
## CD80                 2          6          1          4          3          6
## CD86               965        776        993        839        828        926
## MIX23               17         36         15         43         20         23
## PLS1                15         39          9         29         13         31
## PTX3                49         39        100         47         64         70
## GOLIM4              97         88         81        144         61         96
## MYNN               349        327        191        296        394        334
## TNFSF10           2957       5763       3209       4328       2314       1515
## ADIPOQ               0          0          0          0          0          0
## SPON2              293        152        290        421        597        400
## S100P             3994       3829       1572       2685       3275       3650
## WDR1              6401       6174       5165       6139       6046       5773
## CD38               200        164        150        212        212        178
## PPARGC1A             5          1          7          1          2          1
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          0          0          0          0
## CXCL8            22828      26953      86505      65792      28261      66157
## CXCL2                7          4         19         12          5         14
## AREG                13          4         49          4         47         90
## CXCL10              36         13         53         58         30         23
## CXCL13               1          0          0          0          0          1
## SPP1               123         60         20         26         83         54
## HERC6              197        222        151        247        221        159
## NFKB1              888       1534        731       1542        787        894
## SEC24B             420        640        235        540        476        470
## EGF                 40         18         41         31         25         29
## IL2                  1          0          0          0          1          2
## IL21                 1          1          1          3          2          0
## IL21-AS1             0          2          2          1          2          0
## SLC7A11             15         18         10         16         14          8
## IL15                79         51         60         96         95         57
## EDNRA                0          0          0          0          0          0
## TLR2              3334       5959       2211       4765       1931       3506
## FGB                  0          0          0          0          0          0
## DDX60              464        469        367        541        487        242
## SPCS3             1865       2509        985       2510       1838       2099
## TLR3                 9         25          2         27         12         18
## OSMR                33         31         12         26         29         33
## GZMK               753        678        483       1695       1311       1199
## GZMA              1003        911        687       3109       2413       1822
## ANKRD55             40         99         60         55         23         49
## CENPK               53         22          4         98         31         88
## CAST              2676       2729       2056       2888       2523       2733
## ERAP1             1229        984       1132       1847       1325       1381
## ERAP2             1619       1562       1142        194       2076       1850
## TNFAIP8           1195       1990        668       1820       1111       1426
## CSF2                 0          0          0          0          1          0
## IL5                  0          0          0          0          0          0
## IL13                 1          0          0          1          0          1
## IL4                  6          3          4         11          4          4
## CD14              6727       6439      10973       6573       6883       7437
## CSNK1A1           1394       2685       1185       2028       1358       1334
## PPARGC1B           137        104         97        106        112        117
## TNIP1             5115       4781       4032       4431       4862       4225
## ATOX1              193        162        219        161        208        177
## FAXDC2             175         99        180        176        147        195
## IL12B                1          1          0          0          0          2
## MIR146A              0          0          1          0          0          0
## PDLIM7            1714       1190       1347       1204       1626       1163
## SERPINB1          4104       4370       4202       3666       4090       3577
## SSR1              2496       2724       1471       2543       2499       2382
## CD83               496        153        896        202        344        440
## SOX4               174        155        109        151        204        222
## CMAHP               62         53         39         85         69         77
## HLA-A            44967      32831      46448      38741      72263      44443
## HLA-C           119436      61921      75242      74110      73825      41517
## HLA-B           118763      91281      96417      91106     143978      89225
## MICA                95        154        150        198        155        116
## LTA                 54         79         52        111         35         68
## TNF                293        356        130        260        368        247
## HLA-DRB1          5207       4626       4989       7378       4675       3913
## HLA-DQB1           343       2159       5142       4450        482       3358
## PPARD              303        341        223        357        298        318
## CCND3             3421       3446       4008       5561       3908       4153
## VEGFA              150        160        162        143        241        216
## RUNX2              573       1025        213        421        542        544
## IL17A                1          0          0          1          0          0
## IL17F                0          0          0          0          0          0
## PRDM1              407        994        320        789        620        674
## ATG5               438        405        250        448        508        451
## TRAF3IP2           213        199        128        184        215        167
## NCOA7              351        501        230        637        376        381
## SGK1              2425       4095       1898       1871       1608       2437
## IFNGR1            2959       4849       1391       3300       1867       2459
## TNFAIP3           3107       1288      10865       2064       5692       5693
## SOD2             48988      48946      22401      35873      42821      39584
## LPAL2               13         11         13         17         25         29
## PLG                  0          0          0          2          0          1
## CCR6                65        238         54        185         46         91
## RAC1              2810       3278       2060       2743       2848       3102
## ZNF316             702        354        720        741        864        653
## AHR                891        650        438        884       1085       1082
## IL6                  3          6          8          3          7          1
## TOMM7             2180       2302       2065       2659       2341       2824
## CYCS               526        593        473        676        632        615
## AQP1                 1          2          1          1          6          2
## NT5C3A             854        696        467        604        766        634
## EGFR                 1          1          0          0          0          0
## CD36              2024       2490       3065       2854       2112       2581
## SAMD9             1911       2534       1080       1930       1306       1365
## SERPINE1             7         11         11         12          3         13
## CUX1              1897       1322       1136       1287       1646       1649
## PSMC2              325        455        360        542        348        321
## NAMPT            49625      56933      18217      38523      41560      45742
## HYAL4                0          0          0          0          0          0
## LEP                  5          8          0          3          0          0
## CALD1               18          5         11          8          7         15
## BRAF               675        777        388        759        618        729
## EZH2                43         38         61         55         39         67
## DNAJB6            1632       1541       1132       1459       1515       1452
## CSMD1                8         10          4         34          3          0
## CTSB              6420       4435       7023       5304       6646       5269
## EGR3               694        489       1449        666        416        638
## TNFRSF10A          124        200        119        216        150        166
## BNIP3L            2264       2521       1633       1898       1757       2157
## DUSP4               41         11         17         34         38         98
## NRG1                89         66        216         92        125        147
## RPL7              9189       9926       9980      10982      10694      11430
## IL7                 17         27         12         22         28         10
## GEM                  0          2          1          0          2          2
## MYC                520       1003        290        951        270        468
## GPT                  0          1          3          2          1          2
## JAK2              1072       1208        770       1021        880        819
## CD274              126        239        290        209        205         83
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              3          0          1          1          1          1
## TTC39B             131        217         75        206        130        156
## IFNA1                0          0          0          0          0          0
## TEK                 34         19          1         12         14          5
## TRBV20OR9-2          0          1          0          0          0          0
## TOMM5              208        236        244        342        290        251
## ANXA1             6614       5423       6412       6765       6218       8863
## ERP44             1470       1274       1314       1195       1502       1348
## ZNF483              18         22         14         29         41         25
## TNFSF15              0         10          9         10          3          6
## TLR4              3453       7457       3304       4070       3448       3806
## PTGS1              732        402        941        642        588        984
## HSPA5             7028       4853       7233       6769       6397       6543
## FNBP1             3910       3779       2086       4224       3464       3739
## CARD9              192        121        313        143        117        127
## TRAF2              116        164        113        227        127        120
## CLIC3              119         47         70        129        108        134
## IL2RA              105        124         51        121         51        139
## GATA3              406        328        275        504        320        394
## VIM              18605      13383      17476      12696      13319      16088
## CREM               168        120         91        126        255        227
## DKK1                 1          0          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              713       1055        530       1089        865        818
## PRF1              1720       1654       1083       3916       2222       3203
## ZMIZ1             2856       1956       1318       1905       2168       2314
## IFIT3             4734       4040       5828       2287       5388       1329
## TALDO1            9060       8845       8306       6957       8034       7710
## IGF2                 0          0          0          0          0          1
## INS-IGF2             0          0          0          0          0          1
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1308       1356       1002       1585       1453       1342
## TRIM22            2754       2635       2685       2462       2597       1306
## PTH                  0          0          0          0          0          0
## SAA1                 1          0          0          0          0          0
## SLC1A2               2          3          1          1          4          6
## FOSL1               25          2         72         21         34         36
## CCND1                8         11          8         15          6          5
## JRKL                54        145         65        116         58         65
## MMP7                 0          0          0          0          0          0
## MMP1                 0          0          4          0          0          4
## MMP3                 0          0          0          0          0          0
## CASP1             3689       3177       3605       2774       2752       2373
## DLAT               205        221        111        281        176        183
## IL18               111        105         97         46         93        115
## CD3E              2466       3337       2429       4897       4553       3633
## MCAM               280        298        187        297        272        280
## WNK1              4365       5254       2730       4732       3832       4058
## TNFRSF1A          3559       6349       2968       4228       2643       2760
## GAPDH            21523      16390      20558      15488      18591      19511
## CD4               4487       3654       4514       3803       3733       4391
## SLC2A3            9081      10507       5847       8151       8120       9281
## CLEC4D             516        500        480        269        226        240
## KLRB1              883       1113        615       1265        814       1120
## CD69               856        352       1761        844       1492       1809
## CLEC2B            1750       1896       1477       1716       1791       1462
## OLR1                10         12         12         13         10         17
## ABCD2              121        288         62        262        143        168
## LRRK2             7957      11252       3122       6414       7140       5833
## VDR                403        694        338        366        283        292
## TMBIM6           13950      15972      10348      14388      13053      13244
## PFDN5             3326       3057       3898       3964       3894       3592
## SP7                  0          0          0          0          0          0
## MUCL1                0          1          0          0          0          0
## CD63              2770       2219       3197       2494       2689       2917
## SUOX              1100       1325        870       1056       1001       1037
## RPS26              693        600        824       4437       4473       6937
## RPL41             6789       7128      10256       9808       9470       8336
## IL23A               20         46         19         54         18         30
## DDIT3              581        276        511        374        447        410
## IFNG                18          5         17         28         55         56
## IL22                 0          0          0          0          1          0
## LYZ              86422     104682     122587      73551      90949     122809
## CAPS2                4          3          0          3          6          5
## SYT1                 0          5          4          3          5          2
## BTG1              9187       9394       6725       8707      10584      10487
## HCAR3             2065       5354       4028       3227       1928       2578
## GJB2                 0          0          1          0          2          4
## GJB6                 9         12          8          4         14         27
## TNFSF11              1          5          2          5          1          3
## TPT1             55581      56498      58020      63295      61692      60491
## LMO7                49        136         47        105         42         72
## TNFSF13B          2899       2475       1741       1699       2291       1467
## LAMP1             2639       2565       2354       2772       3011       3085
## PSME2             1563        997       2055       1264       2137       1134
## GZMB               740        576        414       1221       1635       1486
## RPL36AL           2133       1726       1737       2192       2822       2576
## PYGL              4649       5793       3505       4105       3874       3936
## HIF1A             2282       2408       1269       1768       3121       2456
## FOS              27121      40737      77374      30618      36565      44374
## JDP2               931        698        601        489        772        797
## NOXRED1             11         12          3          5          4          3
## SERPINA1         31582      19133      26627      16184      22694      20753
## CDC42BPB           319        194        240        204        209        273
## PLA2G4D              0          0          0          0          0          0
## TRIM69              14         12         21          6         36         15
## SLC51B               0          0          0          0          0          0
## SMAD3              619        662        494       1038        704        758
## CYP1A1               0          0          1          2          0          2
## AKAP13            4603       6344       2605       5497       4739       5644
## MEFV              3411       3531       1524       2271       2692       2235
## SOCS1               47         27         65         46         66         42
## ATXN2L            1861       1263       1590       1993       1918       1884
## CD19               110        149         99        120         93        107
## ITGAL             5744       5326       4740       6674       7173       5799
## ITGAM             4767       4816       4827       5033       5562       6001
## ITGAX             5221       2853       3835       3540       4400       3209
## DNAJA2             566        910        495        901        641        514
## SIAH1              108        213         71        155        134        131
## ADCY7             2639       2357       2007       3048       2735       2557
## NOD2               654        503        799        462        885        706
## CMTM2             2184       2976       2291       1850       1910       1846
## SF3B3              789       1096        817       1314        756        906
## PSMD7              731        721        682        784        737        755
## WWOX                39         36         29         67         56         36
## MAF                372        520        324        636        591        462
## SLC7A5             294        150        114        242        356        347
## CXCL16            3207       1124       1459        873       1834       2262
## XAF1              1119        692       1007        698       1061        503
## CD68              4929       2951       5108       3039       4067       3853
## PER1               565        221        353        279        892        904
## NOS2                 1          0          0          4          0          0
## TRAF4              105        142         75        117        103        106
## CCL2                16         24         23         17          5          6
## CCL5              2509       2403       2826       8687      12381       6846
## CCL3               158        310        418        114        138        219
## CCR7               465       2053        407       1089        310        672
## STAT3             4470       6564       2931       4831       4096       3721
## SOST                 0          0          0          1          0          0
## ITGA2B             490         71        635        188        401        617
## EFCAB13             17         17          8         21         13         23
## NPEPPS             842       1292        683       1145        676        832
## TBX21              227        230        217       1042        762        499
## COL1A1               0          1          1          0          0          0
## MRPS23             171        216        165        287        146        150
## MIR21                5          4          3          6          5          5
## RPS6KB1            328        518        189        513        324        360
## ACE                 56         30         25         66         82         36
## ERN1              1382       1655        547       1560       1469       1576
## PRTN3                5          1          8          5         44         10
## PLIN5               97         66        111         79         56         50
## RETN                58         29         98         55         39         44
## CCL25                0          1          2          0          1          1
## ICAM1             1843        969       2139       1345       2337       1753
## TYK2              1595       1696       1678       1874       1285       1209
## SMARCA4            742        568        645        855        757        707
## ACP5               330        286        282        355        231        255
## JUNB             31759      17829      41520      28498      37225      25345
## CYP4F22             58         12         59         40         49         49
## JAK3              1733       1474       1452       1885       1426       1263
## JUND              7839       2479      19673       3712       9003       6293
## CEBPA             1207        750       1152        765        956        655
## CEBPG              262        360        234        430        296        282
## ACP7                 0          1          0          1          1          3
## ZFP36            16136      21924      42111      15068      19852      18410
## TGFB1             5890       3163       5065       4755       6217       3983
## RPS19             9455       9427      11370      12341      11933      11865
## PSG2                 0          0          0          0          0          0
## FUT2                 0          2          3          5          1          4
## NKG7              2873       2057       2350       7525       9054       5538
## ZNF415               9         19          8          2          3          3
## LILRB2            5319       3181       4799       3012       4629       3982
## LILRA5            3069       2308       3127       1706       3334       1909
## KIR3DL1             85         92         20        202        182        323
## KIR3DL2             41         27          7         95        119         76
## SMOX               112         41        142        121         86        130
## BMP2                 1         10          2          7          3          9
## GINS1                7         13          7         14          5         10
## PLCG1              633       1152        608       1483        741        846
## YWHAB             5723       6206       4891       6129       5543       6387
## PI3               1291        955        757        814        788        588
## MMP9              1837       1907       1556        980       2052       2358
## CD40               133        142        281        216        222        150
## PFDN4               45         55         67         50         44         69
## BMP7                 0          0          0          0          0          0
## RPS21             4447       4725       5354       6007       5318       5391
## MX1               1257       1686       1865        891       1535        527
## PFKL              1291        884       1087       1144       1066        980
## IL17RA            5962       6954       3719       4386       3982       3960
## UBE2L3            1107       1242        904       1326       1014        999
## TPST2             1094        942       1086       1922       1897       1373
## XBP1              1121       1418        751       2293       1371       1081
## UQCR10             563        563        596        674        600        564
## SEC14L2             19         30         18         25         44         31
## APOL6             1489       1518       1217       1718       2016       1290
## APOL1              727        595        852        469        932        474
## TYMP              4325       1693       7768       2770       3672       2329
## BEND2               56         17         52         43         24         80
## PHEX                14         18          8         20          7         10
## TIMP1             1835       1222       1559       1039       1227       1868
## FOXP3               51         51         54         77         44         85
## MSN              26327      25482      17940      23251      25382      26242
## PGK1              9062       7422       7303       7274       8096       8063
## LAMP2             7862       8136       4031       5389       6194       6784
## CD40LG             172        296        123        297        128        173
## IRAK1             1560        909       1382       1289       1826       1449
## COX2             62714      42372      43760      57294      61903      75922
##             GSM3308527 GSM3308528 GSM3308529 GSM3308530 GSM3308531 GSM3308532
## TNFRSF9             91        205         85        133         99        169
## ENO1              5577       5870       7809       6528       5294       4843
## PIK3CD            7422       8557       6347       5774       5518       5516
## PGD               5896       4525       5444       4160       6386       3770
## MTHFR              377        413        413        371        293        463
## TNFRSF1B         13538      13638      14992      15478      14797      12229
## PINK1             1016        810        871        696        848        556
## IFNLR1              56         66         58         89         24         92
## RUNX3             2947       2585       6521       8168       3651       4470
## SH3BGRL3         10970       8198      11427      10505      12441      10730
## CD52              4470       3599       3990       4751       3337       4204
## IFI6              1064       1183        561        582       1286       1121
## ZC3H12A            314        380        452        820        707       1082
## UTP11               81        154        111         81         78         64
## JUN               7541        419        861       9424       1233      31467
## KANK4                1          0          0          0          0          0
## EFCAB7              34         31         30         31         16         20
## IL23R                4          5          4          3          4          9
## ADGRL2               0          0          0          0          0          0
## GBP3               103        280        223        145        101        171
## GBP1               369       1702        699        511        520        378
## GBP5               696       4022       2017       1757       1707       1892
## TGFBR3             543        556       1248       2327        601        945
## VCAM1                0          0          2          6          3          2
## PTPN22             334        503        398        532        231        233
## CD160               53        109        202        101         66        126
## FCGR1A             217        458        415        621        701        378
## MCL1             17168      22302      19167      21743      32488      31672
## CTSK                32         41         32         97         62         63
## RORC                80         74        135         70         49         66
## S100A9          117873     100078      93447     106268     204459      83899
## S100A12           4001       2595       2599       3193       7449       1963
## S100A8           45285      35929      34700      41710      79786      29520
## IL6R              5428       6343       4828       4052       4075       3195
## RIT1              1133       1152       1169       1329       1995       1292
## BGLAP                8          7         10          7          9          9
## IFI16             1724       3974       2064       1562       2206       1156
## AIM2                82        149         89         71        159         37
## CRP                  0          0          0          0          0          0
## FCGR2A           10130      15270      10707       9867      12654       8881
## HSPA6             1604       2628       1193       1179       2396        752
## FCGR3A           19069      20086      15848      14669      16127       6061
## SELL             40397      36546      25949      33152      52298      26857
## GLUL             10372      12403      11247      16273      19594      13598
## PTGS2             3839      15573       2183       2804       2372       6995
## CRB1                 4          1          1          2          2          0
## KDM5B              437        549        342        478        629        467
## IL10                 0          1          3          7          6          3
## YOD1               166        173        244        319        388        277
## HHAT                41         27         45         38         32         47
## TRAF5              318        362        299        333        264        410
## NLRP3              517        692        810        813        885       1075
## LINC01250            0          0          0          0          0          0
## RPS7              9502       7524       9187      10137       9456      10425
## RSAD2              291        730        111        130        348        244
## FOSL2             2775       3403       3357       5826       4789       4363
## REL                770       1188       1033       1222       1232       1251
## TGFA               582        643        407        348        655        383
## DYSF              4991       4869       4081       3463       6745       2419
## HK2               1066       1445        918        688        962        581
## CD8A              1445       1216       1699       3031       1198       2400
## CD8B              1414        803       1000        929        660       1483
## EIF5B              548        680        630        607        381        444
## IL1R1              259        189        188        267        318        249
## RGPD6               80        137         83        103         86         65
## IL1A                 0          0          1          0          0          0
## IL1B               144       1533        171        264        259       1105
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             2840       2020       2256       2487       3113       4210
## NMI               1125       1515       1348       1188       1308        674
## TNFAIP6            596        929        375        226        512        506
## IFIH1              215        593        327        295        301        411
## SCN1A                0          0          0          0          0          0
## ABCB11               0          1          1          1          2          1
## RBM45               44         71         57         52         49         33
## FRZB                 0          0          0          0          0          0
## TFPI                 2          9         10          3          3          7
## STAT1             2304       5607       3112       2544       2865       2442
## NABP1              439        764        279        517        656        762
## SF3B1             4204       4224       4448       4920       5929       4263
## CASP10             262        492        259        242        267        367
## CD28               552        698        504        635        859        773
## CTLA4               52         24         46         87        101         85
## ICOS               173        165        168        171        256        224
## NDUFS1             469        700        455        519        510        374
## CXCR2            17753      31648      18232      14569      20800      13408
## IRS1               117         80        121         76         88        129
## CCL20                0          2          2          1          0         11
## ATG16L1            257        292        280        326        299        372
## GPR35               72         86        155        123        109        100
## PDCD1               39         30         65         48         20         31
## PPARG                1          0          9         10          3          2
## RPL15            15603      11017      15653      14913      14137      16443
## EOMES               62        283        297        245         85        154
## CX3CR1             490       2209       1173        662        233        436
## ACKR2                1          0          4          0          1          0
## CCR2               304       1448        784        443        236        334
## CCRL2               10         51         30         17         41        100
## TLR9                82         93         89         48         52         57
## ARHGEF3            760       1049       1209       1006        953       1413
## ADAMTS9              0          1          0          0          0          0
## TMEM45A              0          1          7          3          0          1
## CD80                 4          5          3          3          2          6
## CD86               681        886        967        716        542        611
## MIX23               24         29         26         24         23         27
## PLS1                25         22         26         32         18         18
## PTX3                37         30         53         79         37         71
## GOLIM4              51        131        108         78         57         48
## MYNN               260        345        292        389        425        430
## TNFSF10           2086       4975       2098       1195       2038       1071
## ADIPOQ               0          0          0          0          0          0
## SPON2              291        363       1061        942        192        399
## S100P             4610       3239       1480       1935       2852        198
## WDR1              5656       6224       7402       5476       4882       3963
## CD38               161        259        216        118        243        244
## PPARGC1A             6         13          2         10          4          4
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          0          0          0          0
## CXCL8            43100      18887       8873      40866      26869     119038
## CXCL2                3          6          3          6          4         53
## AREG                17          2         19        137         73        131
## CXCL10              15         33         22          5         10         17
## CXCL13               0          0          0          0          1          0
## SPP1                34         94          7         74         48         28
## HERC6              245        216        137        149        147        164
## NFKB1              704       1391        970        923        969        826
## SEC24B             418        645        414        459        525        412
## EGF                 27         27         46         32         10         26
## IL2                  0          0          0          0          1          0
## IL21                 0          0          0          0          0          0
## IL21-AS1             1          0          0          0          1          1
## SLC7A11             12          9         11         15         11         16
## IL15                38         88         61         66         46         36
## EDNRA                0          0          0          0          0          0
## TLR2              3765       3303       3036       3553       6568       2605
## FGB                  0          0          0          0          0          1
## DDX60              267        579        222        257        252        238
## SPCS3             1580       2245       2045       2198       1888       1697
## TLR3                 3         18         13         14          3         14
## OSMR                30         38         18         42         48         34
## GZMK               562        566       1243       1754       1096        760
## GZMA               704        935       1862       1983        830       1295
## ANKRD55            117         89         61         46         64         56
## CENPK               81         27         64         32         66        138
## CAST              1965       2442       3083       2325       2026       2818
## ERAP1             1080       1439       1801       1912        805       1508
## ERAP2             2503        167       3582       1660        159       1267
## TNFAIP8           1265       1701       1319       1349       1215       1347
## CSF2                 0          0          2          0          2          1
## IL5                  0          0          0          0          0          0
## IL13                 0          2          0          0          0          0
## IL4                  5         16          3          3          1          1
## CD14              6375       7170       9599      10374       9527       6414
## CSNK1A1           1299       2465       1410       1428       1420       1153
## PPARGC1B            93         94         97        105         88        123
## TNIP1             4931       4566       4890       4423       5149       4210
## ATOX1              210        141        173        174        159        172
## FAXDC2             147        154        225        161        100        158
## IL12B                1          0          0          2          1          1
## MIR146A              0          1          1          0          1          0
## PDLIM7            2110       1268       1636       1566       2517       1418
## SERPINB1          3136       4122       4082       3934       4661       4245
## SSR1              2189       2398       2377       2466       2048       1897
## CD83               297        180        447        306        488       1508
## SOX4               201        133        218        202        164        265
## CMAHP               55         46         41         80         51         86
## HLA-A            35260      42159      49148      45291      43929      41733
## HLA-C            66626      59213      74700      73508     107757      72130
## HLA-B            84037      87641      95814     129678     108955      76298
## MICA               167        194         85        109         87         77
## LTA                 84         61         51         53         53         72
## TNF                200        236        255        312        204        165
## HLA-DRB1          3934       2270       3944       3274       2431       4801
## HLA-DQB1          1088        307        857       2884        337       2778
## PPARD              377        396        362        299        307        301
## CCND3             4555       3497       4870       4953       4834       4010
## VEGFA              213        108        142        186        159        197
## RUNX2              546        547        517        588        747        512
## IL17A                0          0          0          0          0          0
## IL17F                0          0          0          0          0          0
## PRDM1              335        768        710        915        606        465
## ATG5               365        425        393        437        354        309
## TRAF3IP2           271        196        199        187        205        199
## NCOA7              252        463        308        388        405        270
## SGK1              2534       3804       2085       2018       3604       3350
## IFNGR1            2081       4056       2372       2360       2636       1836
## TNFAIP3           2982       1181       3592       9262       6546      18853
## SOD2             29299      44049      38873      39353      56679      39135
## LPAL2                4         16         19         30          5         22
## PLG                  0          1          0          1          0          0
## CCR6                93        157         96         75        108        103
## RAC1              2926       2734       3423       2935       3292       2116
## ZNF316             727        540        699        876        757       1048
## AHR                586        633        949       1550       1638        946
## IL6                  3          3          0          3          3         21
## TOMM7             2864       1950       2426       2914       2215       2114
## CYCS               531        518        610        650        498        840
## AQP1                 1          1          2          6          1          1
## NT5C3A             716        640        634        641        742        595
## EGFR                 0          0          0          0          0          0
## CD36              1750       1860       2477       1967       1261       1167
## SAMD9             1342       2253       1177       1284       1340       1141
## SERPINE1             9         11          6          5          7         12
## CUX1              1656       1510       1617       1696       1563       1412
## PSMC2              249        442        350        334        299        259
## NAMPT            41907      37876      32415      51774      82191      37150
## HYAL4                0          0          4          0          0          0
## LEP                  4          3          2          1          8          1
## CALD1                4         19         14         15          4         10
## BRAF               716        716        637        736        660        741
## EZH2                46         49         40         80         39         67
## DNAJB6            1412       1732       1691       1582       1727       1179
## CSMD1                0          9          8          1          4          0
## CTSB              5105       5239       9230       5836       4610       3624
## EGR3               428        245        435        795       1121        483
## TNFRSF10A          115        160         95        124        132        159
## BNIP3L            2124       2296       1928       2074       2186       1639
## DUSP4               27         21         41        154         84         71
## NRG1                14         91        103         80         36         94
## RPL7             13198       8001      10976      11015      10025      12733
## IL7                  6         18         16         14         14         16
## GEM                  0          1          0          1          1          2
## MYC                633        763        766        320        474        312
## GPT                  0          0          3          1          0          4
## JAK2               888       1125        861        695        909        809
## CD274               46        245         97         99         96         94
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              0          1          3          0          0          1
## TTC39B             164        208        120        142        144        213
## IFNA1                0          0          0          0          0          0
## TEK                  1         75         46         13          5          5
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              190        229        248        249        198        201
## ANXA1             5928       5457       7900       8946       7030       5408
## ERP44             1241       1274       1419       1217       1340       1157
## ZNF483              35         41         19         37         22         50
## TNFSF15              2          3          1          5          2          1
## TLR4              5628       6796       3895       4245       6307       4323
## PTGS1              776        771        980        648        360        639
## HSPA5             4453       3869       8121       6507       7423       7069
## FNBP1             3801       3780       4443       3730       3247       2669
## CARD9               87        185        143        121         70        149
## TRAF2              123        176        122        142        116        107
## CLIC3               64        104        342        155         59        123
## IL2RA               83        115         94         77         75         87
## GATA3              362        364        509        383        248        353
## VIM              17603      11337      19610      16477      20516      16090
## CREM               125        126        183        296        285        175
## DKK1                 0          0          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              581        955        678        880       1024        773
## PRF1              1032       2944       2685       3268       1252       1344
## ZMIZ1             1741       2364       2817       2433       2449       2823
## IFIT3             2762       4706       1649       1117       2781       2651
## TALDO1           10536       9616       9529       7853      11851       7496
## IGF2                 1          1          0          0          0          0
## INS-IGF2             1          1          0          0          0          0
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1333       1292       1608       1404       1172       1284
## TRIM22            1316       2838       1471       1435       1509       1268
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          0          0          0          0
## SLC1A2               1          0          1          2          8          3
## FOSL1               28          7         22         51        110         69
## CCND1                5         14          7          6          5          8
## JRKL                88        126         68         66         43         66
## MMP7                 0          0          0          0          0          0
## MMP1                 0          2          2          0          0          0
## MMP3                 0          0          0          0          0          0
## CASP1             1912       3394       2397       1853       3069       1562
## DLAT               201        197        243        187        128        138
## IL18                83         96         73         97         90         77
## CD3E              4147       2859       3938       4460       2571       4195
## MCAM               253        219        230        307        215        302
## WNK1              4015       4963       4140       3872       3511       4211
## TNFRSF1A          2956       5062       4123       2924       3793       2899
## GAPDH            18810      14484      21199      20942      21171      14966
## CD4               3666       3783       3771       2505       2692       3516
## SLC2A3           10259       5065       8341       7020      15963       9088
## CLEC4D             322        319        202        337        502        186
## KLRB1             1084        746       1192       1581       1422       1434
## CD69              1299        231       1060       1910       1209       6309
## CLEC2B            1242       1611       1302       1434       2037       1418
## OLR1                 7          6          6         88          5         13
## ABCD2              139        253        128        142        161        185
## LRRK2             6652       9527       5947       5202       8587       4311
## VDR                409        633        368        326        517        333
## TMBIM6           13347      14363      14338      12145      13557      11928
## PFDN5             3486       2824       3480       3456       3750       3987
## SP7                  0          0          0          0          0          2
## MUCL1                0          1          0          0          0          0
## CD63              2635       2223       2856       3248       3356       2562
## SUOX              1032       1299       1125       1025        917        772
## RPS26             4269       5067       4171        877       6495        763
## RPL41             8601       6561       8850       8649       7871       9740
## IL23A               40         47         24         34         46         51
## DDIT3              424        229        422        443        826        725
## IFNG                12          8          9         42         16         74
## IL22                 0          0          0          0          0          1
## LYZ             101968      37839      66522      78408      48341      71176
## CAPS2                6          8          6          5          3          4
## SYT1                 2          3          0          8          6          3
## BTG1              9648       8330       8181      10595      10126      14324
## HCAR3             2406       2520       2062       1654       2795       4374
## GJB2                 0          0          1          0          0          2
## GJB6                14          2          6         11         37          9
## TNFSF11              0          7          1          1          3          2
## TPT1             65216      26276      59038      57818      57005      67118
## LMO7                87         88         72         46         74         65
## TNFSF13B          1230       2260       1613       1777       1899       2208
## LAMP1             3056       2704       3197       3038       2971       2541
## PSME2              908       1283       1308       1080       1031       1003
## GZMB               434        926       1358       1793        420       1153
## RPL36AL           2704       2103       2287       2667       2272       2026
## PYGL              5636       4580       4729       3708       7481       3083
## HIF1A             1310       2283       1741       2590       4343       3173
## FOS              57739      20194       4170      33439      13675      82548
## JDP2               885        583        759        807       1115        662
## NOXRED1             10          6          4          8          6         11
## SERPINA1         18805      17291      21779      22363      23192      26026
## CDC42BPB           142        283        232        224        170        229
## PLA2G4D              0          0          0          0          0          0
## TRIM69               6         18         19         18         10          7
## SLC51B               0          0          0          0          0          0
## SMAD3              534        613        720        843        552        651
## CYP1A1               0          0          0          1          0          1
## AKAP13            3774       5321       4304       4936       5082       3819
## MEFV              2316       4064       3294       2432       2522       1772
## SOCS1               53         25         49         55         36        141
## ATXN2L            1933       1541       2131       1935       1385       1995
## CD19                76        138        126         99        102        184
## ITGAL             4134       4985       6016       6710       4620       4805
## ITGAM             5717       4725       6015       5687       6702       4091
## ITGAX             3461       3419       3678       5294       7566       5273
## DNAJA2             537        844        606        531        716        652
## SIAH1               86        198        101        128        160        128
## ADCY7             2515       2662       3402       2704       1992       2299
## NOD2               276        566        673        361       1003        864
## CMTM2             2591       2542       1700       1962       4285       1977
## SF3B3              761       1094       1080        789        564        911
## PSMD7              655        743        681        696        829        596
## WWOX                45         39         65         49         62         48
## MAF                328        388        427        606        271        483
## SLC7A5             190        137        405        294        412        260
## CXCL16            1547       1317       1690       1959       2878       2198
## XAF1               584        899        644        535        582        538
## CD68              3225       3415       4959       3302       3317       2505
## PER1               482        241        597       1270       1696       1349
## NOS2                 3          0          0          1          0          5
## TRAF4               82         93        112        125        102        168
## CCL2                 8         19          7         11         12          6
## CCL5              2363       2583       5819       9185       2758       5437
## CCL3                60        211         35         72         33        740
## CCR7              1175       1522        629        386        743        871
## STAT3             3922       6267       4476       3887       4494       2974
## SOST                 0          0          0          0          0          0
## ITGA2B             273        365        824        302        181        260
## EFCAB13             32         25         26         18         22         27
## NPEPPS             756       1108        821        724        900        747
## TBX21              172        360        509        774        201        476
## COL1A1               1          1          0          0          0          2
## MRPS23             138        210        189        167        147         87
## MIR21                6          5          7         13          5          7
## RPS6KB1            354        462        377        379        374        314
## ACE                 38         42         67         77         93         46
## ERN1              1087       1485       1324       2222       1519       1398
## PRTN3                6          4         11         31          3         10
## PLIN5               85         96         79         80         98        104
## RETN                54         40         90        188         61         56
## CCL25                0          1          3          1          0          0
## ICAM1             1061       1150       1489       1494       2460       2943
## TYK2              1497       1874       1526       1563       1188       1348
## SMARCA4            787        726        841        815        594        719
## ACP5               209        272        467        222        180        280
## JUNB             33970      15952      12555      32964      35821      32053
## CYP4F22             11         52         34         18         16         22
## JAK3               978       1716        998       1645       1830       1962
## JUND             10655       2390       6677       7916       6604      25113
## CEBPA              913        690       1071       1041       1010        494
## CEBPG              214        335        322        284        269        239
## ACP7                 1          0          1          1          1          0
## ZFP36            16542      14747       8075      17819      13352      32898
## TGFB1             5736       3501       8274       5578       5869       4838
## RPS19            11102       8579      12304      11587      10389      12171
## PSG2                 0          0          0          0          0          0
## FUT2                 5          2          2          1          4          5
## NKG7              2190       2728       5354       8312       2213       5967
## ZNF415               9         12          7          8          3         22
## LILRB2            4003       3592       4388       3796       4945       4082
## LILRA5            2575       2099       2871       2018       3685       1997
## KIR3DL1             31         28        264        217         37         82
## KIR3DL2             23         68         59         79         17         45
## SMOX               112         93        157        106         65        150
## BMP2                 3          9          0          4         10          3
## GINS1                6         12          3          9         10          2
## PLCG1              909        899        819        851        708        880
## YWHAB             5560       6621       6698       6181       5528       4819
## PI3                348       1025        880        717       1146        620
## MMP9              3888       1931       1995       2148       5709        566
## CD40                98        126        181         88        101        101
## PFDN4               44         52         45         67         72         64
## BMP7                 0          0          0          0          0          0
## RPS21             6370       4013       5684       5649       5242       6143
## MX1               1281       2255        516        415       1024       1059
## PFKL              1025       1252       1427       1051        842        935
## IL17RA            5985       6817       5698       4345       5519       3274
## UBE2L3            1035       1110       1237        953        981        732
## TPST2             1237        913       1746       1708       1144       1227
## XBP1               823       1381       1664       1202       1230        902
## UQCR10             529        540        668        569        543        420
## SEC14L2             82         13         35         45         36         62
## APOL6              641       2440       1075       1233       1123        991
## APOL1              362       1080        729        476        475        480
## TYMP              2951       3907       4192       2905       2887       2320
## BEND2               65         41         79         33         20         43
## PHEX                13         13         23          6          2         22
## TIMP1              996       1933       1879       1857       2783       1218
## FOXP3               78         71         55         68         43         62
## MSN              25884      23598      29667      25346      28530      21476
## PGK1              7117       7060       7848       8427       9359       6684
## LAMP2             7881       7143       6309       6240       8092       5330
## CD40LG             226        268        178        159        134        118
## IRAK1             1549       1090       1841       1893       1518       1485
## COX2             62176      48013      67885      58774      44794      57900
##             GSM3308534 GSM3308535 GSM3308536 GSM3308537 GSM3308538 GSM3308539
## TNFRSF9            142        133         77         97        184        166
## ENO1              5491       6502       6299       6624       6847       8162
## PIK3CD            7220       6685       7445       6432       5920       6378
## PGD               4300       4487       5968       5086       4672       5467
## MTHFR              584        413        360        388        474        406
## TNFRSF1B         12408      10891      16164      12847      12347      12645
## PINK1              681        642        783        709        682        787
## IFNLR1              57         42         62         50         79         48
## RUNX3             4066       3307       2798       3517       4758       2429
## SH3BGRL3          9405       8684      11228      10738      11069      10639
## CD52              5375       3953       3752       5399       5953       3765
## IFI6              1011        892       3096        593       1020        511
## ZC3H12A            505        447        508        675        421        701
## UTP11               82        118        111        101        121        134
## JUN              21511       8569       4494       7318       8452      11637
## KANK4                1          0          0          1          0          0
## EFCAB7              42         38         28         17         35         24
## IL23R               10          0          4          2         11          3
## ADGRL2               0          0          1          0          1          0
## GBP3               276        315        190        219        228        144
## GBP1               719       1709       1413        553        713        674
## GBP5              1909       4611       3145       2664       2863       1254
## TGFBR3             544        685        549        521        939        309
## VCAM1                2          4          2          0          3          1
## PTPN22             388        464        438        351        520        303
## CD160              214        222         32         74        275        136
## FCGR1A             406        996        585        522        432        721
## MCL1             23689      23615      24264      21820      17344      22244
## CTSK                81         45         59         58         50         71
## RORC                77         35         61         55         72         47
## S100A9           99827      95727     116372     113883      92054     136886
## S100A12           3449       2773       2487       3177       2287       3595
## S100A8           39625      38390      42997      42504      33315      55654
## IL6R              4106       4348       4793       3894       3612       2546
## RIT1              1062        937       1458       1667       1035       1491
## BGLAP                9          8         10          5          7         13
## IFI16             2180       3045       3897       1749       2606       2492
## AIM2               153        108        125         74        137        119
## CRP                  0          0          0          0          0          0
## FCGR2A           11754      11015      14864      10970       8629      15900
## HSPA6             1614       1848       2389       1388       2290       1853
## FCGR3A           14421      10612      21185      14348      17373      15192
## SELL             32955      36599      40746      27746      25838      33086
## GLUL             12042      12619      26321      20318      13072      18752
## PTGS2            14331      28297       6435       4718       4561      29543
## CRB1                 0          1          0          0          0          0
## KDM5B              426        392        620        441        360        448
## IL10                 7          1          5          4          4          3
## YOD1               219        208        226        343        231        192
## HHAT                33         40         29         26         45         34
## TRAF5              458        380        309        343        533        369
## NLRP3              777        472        773        916        515       1403
## LINC01250            1          0          0          0          1          0
## RPS7              8845       8137       7902      11638      12392       8312
## RSAD2              387        375       2582        119        337        147
## FOSL2             3234       2888       4248       5509       2590       2376
## REL               1005        943       1053       1143        931        862
## TGFA               482        575        831        627        388        515
## DYSF              4199       4272       4265       3427       2732       4741
## HK2                961       1441       1263        916        802        969
## CD8A              1121       2271       1179        989       2729        395
## CD8B               762       1023        648        641       1421        458
## EIF5B              495        586        637        387        584        422
## IL1R1              201        223        250        289        191        272
## RGPD6               57         73         66         76         79         47
## IL1A                 1          2          0          0          0          1
## IL1B              1365       2055        659        420        375       5000
## IL37                 0          0          0          0          0          0
## IL36RN               0          0          0          0          0          0
## IL1F10               0          0          0          0          0          0
## IL1RN             2540       2319       4508       2516       1431       4998
## NMI               1356       1580       2227       1569       1238       1589
## TNFAIP6            522        714        541        242        274        336
## IFIH1              376        494        607        233        364        299
## SCN1A                0          0          0          0          0          0
## ABCB11               0          0          0          0          2          3
## RBM45               57         61         68         55         82         47
## FRZB                 0          0          0          0          0          0
## TFPI                 2          1          3          2          2          2
## STAT1             3140       6044       6416       4059       4773       3337
## NABP1              718        833        909        464        544        847
## SF3B1             4243       5200       5605       5746       4598       5139
## CASP10             385        376        345        364        434        427
## CD28               658        708        884        740        657        503
## CTLA4               75         40         89         90         86         26
## ICOS               135        171        179        130        147        125
## NDUFS1             453        607        575        497        655        583
## CXCR2            18096      20566      19235      14831      12093      25371
## IRS1                93         42         82         71         91         72
## CCL20                7          5          2          4          4         12
## ATG16L1            316        348        368        346        404        290
## GPR35               62         65        114        164        104        122
## PDCD1               50         23         30         18         60         20
## PPARG                8          1          1          5          4          7
## RPL15            13829      12528      12457      18160      17973      13795
## EOMES              134        314        107         51        257         91
## CX3CR1            2331       2381        742        538       1431       1709
## ACKR2                1          2          4          2          1          1
## CCR2               613        712        449        315        470        957
## CCRL2               30         36         54         46         37         36
## TLR9                59         52         80         56         76         76
## ARHGEF3           1199       1364       1376       1071       1506       1027
## ADAMTS9              0          0          0          0          0          0
## TMEM45A              1          0          4          1          1          0
## CD80                15          3          4          5          4          2
## CD86               786        658        918       1128        947       1035
## MIX23               33         33         37         19         40         25
## PLS1                23         26         15         14         26         12
## PTX3                42         62         52         57         42         82
## GOLIM4              85         95         73         76         97         92
## MYNN               300        351        473        372        339        322
## TNFSF10           2554       3460       3864       1373       2058       3132
## ADIPOQ               0          0          0          0          0          0
## SPON2             1042        440        314        392        872        453
## S100P             1812       1905       5396       3323       1587       3690
## WDR1              5241       6255       6498       5101       6057       5688
## CD38               419        299        356        233        436        218
## PPARGC1A             5          0          2          7          8          5
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          0          0          1          0          0
## CXCL8            86428      68609      26530      66279      26599     149192
## CXCL2               29         38         13         26         19        179
## AREG                39         19         31         97         13         24
## CXCL10              24         37         31         16         46         22
## CXCL13               0          1          1          0          1          1
## SPP1                32         13         49         49         49         68
## HERC6              218        148        315        128        206        182
## NFKB1              886       1027       1065        873        912        969
## SEC24B             374        405        547        507        441        452
## EGF                 14         18         20         16         14         14
## IL2                  0          0          0          0          0          1
## IL21                 2          2          0          0          1          0
## IL21-AS1             1          1          0          1          2          0
## SLC7A11             11         10         17          3         10          8
## IL15                76         80        103         57         91        100
## EDNRA                0          0          0          1          0          0
## TLR2              3021       2978       3024       2343       2064       4213
## FGB                  0          0          0          0          0          0
## DDX60              354        507        792        186        401        190
## SPCS3             1609       1998       2286       1799       2031       1989
## TLR3                10         19          9          6         18          3
## OSMR                25         16         43         33         17         25
## GZMK               555        509        545        284       1119        324
## GZMA              1346       1296        941        623       2070        618
## ANKRD55             92        140        116         68        145         56
## CENPK               16         15         77         18         28        106
## CAST              2972       2357       2349       2324       2717       2841
## ERAP1             1509       1500       1263       1096       1907       1119
## ERAP2             1535       1809       1585       1363        235       1268
## TNFAIP8           1441       1527       1793       1198       1685       1302
## CSF2                 1          0          0          0          0          0
## IL5                  0          0          0          0          0          0
## IL13                 1          0          0          0          2          0
## IL4                  6          9          7          0          1          0
## CD14              7825       6926       8542      10042       8622      11966
## CSNK1A1           1497       1784       1756       1379       1633       1680
## PPARGC1B           131        124        130        142        122        118
## TNIP1             4618       4297       4761       4016       3783       4429
## ATOX1              182        151        205        220        194        195
## FAXDC2             126        176        162        145        121        112
## IL12B                3          1          1          0          0          2
## MIR146A              0          0          0          0          1          0
## PDLIM7            1564       1427       2017       1653       1348       1932
## SERPINB1          4199       3636       4580       4670       4131       5234
## SSR1              2001       2174       2534       2206       2222       2352
## CD83               631        648        712        437        469        965
## SOX4               153         85        122        318        174        148
## CMAHP               41         96        106         69        144         47
## HLA-A            40753      40633      61216      42700      39964      40864
## HLA-C            44667      63359      90590      84364      57073      66543
## HLA-B            76554     113185     124363     119087      97423      84345
## MICA               231        196        121        116        144        157
## LTA                 95         98         60         60        120         61
## TNF                162        238        226        408        323        399
## HLA-DRB1          2941       5077       7279       4820       4513       3950
## HLA-DQB1           255       2592       3770        477        838       1416
## PPARD              327        294        368        380        386        309
## CCND3             4184       4264       3708       4234       4170       4208
## VEGFA              158        153        219        217        113        204
## RUNX2              508        368        645        598        422        618
## IL17A                0          0          0          0          0          0
## IL17F                0          0          0          0          0          0
## PRDM1              446        516        469        400        562        449
## ATG5               322        376        493        452        432        355
## TRAF3IP2           186        220        163        229        232        197
## NCOA7              310        313        341        282        364        313
## SGK1              2899       3993       6094       2828       3231       6591
## IFNGR1            2167       2282       3668       2864       2304       2800
## TNFAIP3           3893       4186       2647       5143       2210       9325
## SOD2             38035      36651      51551      46224      26703      37167
## LPAL2               14         17          9          9         25         20
## PLG                  1          0          1          1          0          1
## CCR6               121        105         87         96        128         95
## RAC1              2499       2721       2864       2722       2663       3157
## ZNF316            1023        711        807        817        883        585
## AHR                946        621       1389       1033        737        949
## IL6                 12          2          2          4          0          2
## TOMM7             2001       1670       1874       1942       1995       2041
## CYCS               774        655        577        520        635        586
## AQP1                 5          3          3          2          1          1
## NT5C3A             556        635        945        583        567        555
## EGFR                 0          0          0          0          0          1
## CD36              2054       1369       1739       1677       1689       3541
## SAMD9             1956       2562       2442        887       1485       1492
## SERPINE1            10         16          8         11          8         18
## CUX1              1433       1184       1535       1746       1330       1296
## PSMC2              329        395        365        341        455        405
## NAMPT            30331      32360      73409      55636      29997      44135
## HYAL4                0          0          0          0          0          0
## LEP                  6          8          6          3          2          3
## CALD1                8         11         24          4          3          6
## BRAF               651        658        736        631        576        547
## EZH2                53         50         81         46         78         60
## DNAJB6            1237       1512       1511       1779       1342       1601
## CSMD1                1          0         34          0          0          2
## CTSB              4713       3925       5649       5576       5213       6681
## EGR3               825       2185        915        299        480       1294
## TNFRSF10A          194        201        185        171        196        167
## BNIP3L            1754       1979       2794       2467       1975       2730
## DUSP4               41         26         55         58         49         57
## NRG1               108         45        107        103         68        323
## RPL7             10503       9359       9691      13341      11971       9422
## IL7                 17         10         11          8         16         17
## GEM                  0          2          1          0          1          2
## MYC                682        822        813        593        887        690
## GPT                  5          1          4          1          3          1
## JAK2               937        805        995        604        795        979
## CD274              126        199        182        101        133        169
## IL33                 0          0          0          0          0          0
## LURAP1L-AS1          0          0          0          0          0          0
## LURAP1L              0          2          1          1          1          0
## TTC39B             179        223        196        129        191        139
## IFNA1                0          0          0          0          0          0
## TEK                  8         18         19         15         32         20
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              239        243        205        206        266        193
## ANXA1             5767       4384       6561       7746       6869       7084
## ERP44             1138       1218       1564       1304       1354       1305
## ZNF483              33         49         35         26         35         21
## TNFSF15              8          7          6          1          6          2
## TLR4              5126       6306       7582       4028       3883       5117
## PTGS1              531        666       1061        631        473        424
## HSPA5             6985       7850       6225       5102       4159      10847
## FNBP1             2967       3396       3699       3549       3828       3365
## CARD9              212        129        152        147        193        228
## TRAF2              153        174        145        131        167        136
## CLIC3              189        121         79        132        258        111
## IL2RA              124         81        120         66        109         74
## GATA3              387        432        346        264        439        406
## VIM              15150      13125      15177      16488      17169      21654
## CREM               139        134        192        253        138        121
## DKK1                 0          0          0          0          0          0
## MBL2                 0          0          0          0          0          0
## SAR1A              669        723       1218       1041        887        776
## PRF1              3511       3838       2368       1826       5550       1564
## ZMIZ1             2144       1558       2120       2562       1917       2075
## IFIT3             3353       4789      12052       1658       2519       2440
## TALDO1            8076       8102      11132       9449       8190      11454
## IGF2                 0          0          1          0          0          0
## INS-IGF2             0          0          1          0          0          0
## IGF2-AS              0          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             1278       1379       1336       1393       1400       1240
## TRIM22            2006       2761       3500       1796       2693       1977
## PTH                  0          0          0          0          0          0
## SAA1                 0          0          0          0          1          1
## SLC1A2               2          3          1          1          0          1
## FOSL1               42         27         82         47         23         73
## CCND1                9         11         13          6          9          3
## JRKL               113        128         86         57        101        102
## MMP7                 1          0          0          0          0          0
## MMP1                 1          1          2          0          0          3
## MMP3                 0          0          0          0          0          0
## CASP1             2352       2523       3008       2513       2723       3048
## DLAT               202        230        199        156        279        223
## IL18                97         68         77        122         97         79
## CD3E              3339       4032       3433       3081       4890       2223
## MCAM               230        239        282        245        204        168
## WNK1              3523       4183       3274       2939       3482       3492
## TNFRSF1A          3126       3068       4285       2674       2921       3869
## GAPDH            14617      14151      16104      21197      18042      19713
## CD4               3235       3156       4439       5020       4492       5016
## SLC2A3            8489       7734      13576       9966       6135       8405
## CLEC4D             174        424        364        262        153        288
## KLRB1             1016        559        857        904       1674        647
## CD69              3131       3235       1860       1646       1708       3387
## CLEC2B            1359       1664       1967       1577       1583       1741
## OLR1                 2         16          7         10         11         77
## ABCD2              173        243        251        154        226        153
## LRRK2             6394       7042       7446       6423       4586       6563
## VDR                353        432        476        386        374        383
## TMBIM6           12150      13397      15019      12233      13472      13572
## PFDN5             3367       2979       3301       4599       4432       3430
## SP7                  0          0          1          0          1          0
## MUCL1                0          1          0          0          0          0
## CD63              2358       2310       2952       3125       2757       3093
## SUOX               868       1051       1227        942       1174       1011
## RPS26             3734       3414        762       8181       1017       3398
## RPL41             7883       7325       7090       9574       9590       7185
## IL23A               55         53         52         49         48         39
## DDIT3              617        585        806        798        436        949
## IFNG                78         76         23         18         73         89
## IL22                 1          1          0          0          0          0
## LYZ              44429      77805      69418      90564      70541      95311
## CAPS2                5          8         10          4          4          7
## SYT1                 3          1          1          0          6          1
## BTG1              9541      11025      10276      10904       9613      11145
## HCAR3             3630       3483       2386       1643       1841       3511
## GJB2                 1          0          3          6          1          1
## GJB6                26         10         43         39         12         17
## TNFSF11              4          2          5          4          1          0
## TPT1             53226      47553      55228      74936      68105      57079
## LMO7                82        109         87         80        108         68
## TNFSF13B          1925       1593       3459       2495       1639       2178
## LAMP1             2695       2824       3227       2646       3112       2806
## PSME2             1221       1413       1609       1565       1822       1119
## GZMB              1374        835        551       1057       1337        546
## RPL36AL           2195       2197       2595       2350       2425       1617
## PYGL              4055       4364       6475       4920       3715       5540
## HIF1A             1738       1709       3821       3659       1573       1773
## FOS              89861      55929      33126      63782      37029      61814
## JDP2               598        611        854        884        662        860
## NOXRED1             11          8          6          5          5          6
## SERPINA1         20937      20812      25612      22967      16486      27542
## CDC42BPB           220        157        179        285        230        317
## PLA2G4D              0          0          0          0          0          0
## TRIM69              13         22         17         10         18         10
## SLC51B               0          0          0          0          0          0
## SMAD3              681        539        657        669        819        528
## CYP1A1               1          1          1          0          2          3
## AKAP13            3551       4597       4066       4005       3684       2750
## MEFV              2052       2365       2997       2419       2375       3192
## SOCS1              112         83         89         42         60         34
## ATXN2L            1950       2023       1864       1878       2316       1967
## CD19               258        145         83        115        209         93
## ITGAL             5475       6418       5300       4180       6253       5493
## ITGAM             4343       4701       5653       4722       3813       4585
## ITGAX             4744       3887       5658       5786       4309       5621
## DNAJA2             547        718        716        589        750        777
## SIAH1               99        121        154        166        130        110
## ADCY7             2930       2412       1991       2056       2593       2305
## NOD2               414        464        470        433        677        494
## CMTM2             2158       1902       3113       2095       2001       2343
## SF3B3              863       1240        982        710       1160        978
## PSMD7              660        631        798        849        700        647
## WWOX                31         41         40         66         61         51
## MAF                457        598        473        289        512        391
## SLC7A5             213        221        269        380        255        160
## CXCL16            2069       1399       2023       3345       1712       2435
## XAF1               845       1042       1504        554        991        543
## CD68              3098       3212       3502       5177       4572       4983
## PER1               488        390        729       1401        502        532
## NOS2                 2          0          0          7          0          5
## TRAF4              130        120         75        138        152         83
## CCL2                21         29         47          7         28          9
## CCL5              3322       4942       2836       2378       6028       1531
## CCL3               423        556        164        377        303       1749
## CCR7              1143       1376       1020        863       1423        716
## STAT3             3586       5080       5528       4393       3700       4702
## SOST                 0          0          0          0          0          0
## ITGA2B             190        423        609        183         85        220
## EFCAB13             26         26         12         22         17         18
## NPEPPS             712        895        934        762        858        963
## TBX21              487        571        255        289        595        255
## COL1A1               1          2          1          0          3          1
## MRPS23             180        179        169        167        252        178
## MIR21                2          4         10          7          5          3
## RPS6KB1            368        380        366        321        446        329
## ACE                 44         42         46         48         37         20
## ERN1               822       1074       1554       1348       1340        976
## PRTN3                9          6          0          3          9         30
## PLIN5              105         70        144        116         72        121
## RETN                53         66         24         69         84        142
## CCL25                0          1          0          0          0          0
## ICAM1             1679       1279       2040       2404       1457       2131
## TYK2              1858       1867       1956       1770       1990       2288
## SMARCA4            821        802        638        656        847        757
## ACP5               256        359        169        369        300        211
## JUNB             40161      26651      38192      49607      34696      50002
## CYP4F22             51         66         23         20         57         41
## JAK3              1851       1899       2191       2072       1698       2103
## JUND             17105       8939       5781       7163       7401       9792
## CEBPA              749        612        766       1050        848        797
## CEBPG              246        278        261        279        298        325
## ACP7                 0          1          0          1          0          2
## ZFP36            30462      23969      31430      39018      20574      81946
## TGFB1             5006       4136       5128       4911       6176       5393
## RPS19            11690      10230       9196      11642      13321       9574
## PSG2                 0          0          0          0          0          0
## FUT2                 6          1          4          3          2          3
## NKG7              4447       4783       2466       2588       6018       2319
## ZNF415               6          6          6         12         22          1
## LILRB2            5193       3686       4865       4468       4225       5267
## LILRA5            2906       2264       2800       1771       2853       2995
## KIR3DL1            143          4         31        281         59         54
## KIR3DL2            118         19         44         28         78          9
## SMOX                71         93        114         94         57         65
## BMP2                 6          9          6          4          1          8
## GINS1                7         10         16         10         12          6
## PLCG1              934       1052        999        889       1154        849
## YWHAB             5473       5924       6703       5522       6079       5922
## PI3               1034        688        580        863        822       1480
## MMP9              1240       3027       2280       1336       2044       2225
## CD40               216        138        129        138        305        119
## PFDN4               53         45         49         66         61         59
## BMP7                 0          0          0          0          0          0
## RPS21             5047       4763       4347       6234       6371       4775
## MX1               1106        850       3861        622       1061        519
## PFKL              1293       1195       1125       1198       1344       1432
## IL17RA            4963       4853       5317       4635       4253       4513
## UBE2L3             960       1076       1125        962       1189       1077
## TPST2             1417       1105       1037        871       1438       1187
## XBP1               827       1113       1133       1069       1211        979
## UQCR10             544        536        533        572        676        582
## SEC14L2             66         30         52         56         24         36
## APOL6             1238       2454       1685       1062       1311       1090
## APOL1              572        914        900        483        665        488
## TYMP              2862       2864       2979       3007       3648       4283
## BEND2               18         67         64         38         24         39
## PHEX                 7         13         15         14         17          6
## TIMP1             1228       1201       1330       1791       1659       1239
## FOXP3               86         76        101         91         92         58
## MSN              20915      24110      26981      23939      24167      25502
## PGK1              6735       6380       8424       8628       7214       8132
## LAMP2             5289       6149       8736       6100       5262       7156
## CD40LG             188        341        167        119        243        217
## IRAK1             1488       1303       1329       1498       1529       1268
## COX2             62507      47099      49513      76405      69573      43619
##             GSM3308540 GSM3308541 GSM3308542 GSM3308543 GSM3308544
## TNFRSF9            149        119        138         91         71
## ENO1              8082       6185       4198       6697       5843
## PIK3CD            6555       6861       4961       5293       5306
## PGD               7592       4594       3824       3656       3689
## MTHFR              399        665        299        399        354
## TNFRSF1B         18265      13258      10760      11125      14567
## PINK1              648        711        386        547        733
## IFNLR1              34         71         42        112         62
## RUNX3             3568       3987       2381       4812       4413
## SH3BGRL3         12382       9825       7460       9860      12493
## CD52              4251       4285       1896       5050       4696
## IFI6              1041        836      18406        807       1644
## ZC3H12A            605        343       1077        667       1324
## UTP11              115        112         94        117         78
## JUN               6473       6316       3791      27941      29549
## KANK4                0          0          0          0          0
## EFCAB7              17         31         18         36         16
## IL23R                0          3          0          8          9
## ADGRL2               0          0          1          0          0
## GBP3               133        176        443        212         74
## GBP1               770        713       8455        693        753
## GBP5              2370       1932      15479       2452       2791
## TGFBR3             649        700        449        972       1049
## VCAM1                0          4          0          6          1
## PTPN22             445        464        227        424        213
## CD160              137        166         74        185        130
## FCGR1A            1122        365       2103        405        957
## MCL1             21964      17933      43302      20044      27363
## CTSK                73         67         61         44         49
## RORC                27         59         21         82         64
## S100A9          133352      80372     137617      74733     121556
## S100A12           3843       1977       4829       1642       2694
## S100A8           48649      27959      54159      28840      46880
## IL6R              4431       3548       2712       2745       3827
## RIT1              1517       1033        872       1053       1372
## BGLAP                9          6          4          6          8
## IFI16             2206       2611      11229       2053       1242
## AIM2               103         79        581         71         65
## CRP                  0          0          0          0          0
## FCGR2A           11590      11027      16116       8629       9486
## HSPA6             1683       1872       1932       2105        911
## FCGR3A           13062      11225      19621      11789      14426
## SELL             40912      24719      46185      26471      22038
## GLUL             19628      14826      23969      11619      16996
## PTGS2             1503       3056      38941      21162       8863
## CRB1                 0          0          0          3          1
## KDM5B              407        408        218        400        450
## IL10                13          4         16          5          4
## YOD1               318        244        148        224        227
## HHAT                35         46         26         75         48
## TRAF5              283        493        175        444        294
## NLRP3              919        662       2155        827       1121
## LINC01250            0          0          0          0          0
## RPS7              9128      10047       4520       9744       9566
## RSAD2              316        202      25652        252        353
## FOSL2             2964       2969       3673       3046       6409
## REL               1290       1078        786       1124       1020
## TGFA               446        376        496        326        499
## DYSF              4344       2515       7757       2501       3344
## HK2               1087        710        963        908        888
## CD8A               603       1804       1168       3399       1755
## CD8B               238        644        491       1296        690
## EIF5B              487        514        289        593        390
## IL1R1              203        257        272        135        222
## RGPD6              103         93         48         93         65
## IL1A                 0          0         16          8          1
## IL1B               471        459      10913       2691       1321
## IL37                 0          0          0          0          0
## IL36RN               0          0          0          0          0
## IL1F10               0          0          0          0          0
## IL1RN             1879       1632      48817       3704       4845
## NMI               1649       1331       3758        938        954
## TNFAIP6            263        259       2585        381        176
## IFIH1              323        288       3603        379        351
## SCN1A                0          0          0          0          0
## ABCB11               0          2          3          0          0
## RBM45               62         86         42         63         47
## FRZB                 0          0          0          0          0
## TFPI                 5          4          2          2          5
## STAT1             4070       3749      12872       4511       2592
## NABP1              561        565       1317        675        384
## SF3B1             5433       4549       4881       4658       3636
## CASP10             368        349        555        341        268
## CD28               730        852        324       1015        590
## CTLA4              100        109        104        101         57
## ICOS               152        152        272        186        122
## NDUFS1             558        561        422        579        374
## CXCR2            18872      17158      21640      12622      13087
## IRS1                61         86         44         60         69
## CCL20                0          2         12         25         23
## ATG16L1            311        425        189        428        334
## GPR35              108        108        101         75        142
## PDCD1               35         76         37         72         52
## PPARG                5          2          0          4          0
## RPL15            15033      16085       8137      15291      14986
## EOMES               70        156         95        196        112
## CX3CR1             932       1064        665       1159        517
## ACKR2                2          2          0          2          0
## CCR2              1102        712        477        476        386
## CCRL2               77         33         65         57         39
## TLR9                71         73         41         44         45
## ARHGEF3           1181       1216        934       1808        887
## ADAMTS9              0          0          0          0          0
## TMEM45A              0          1          1          1          2
## CD80                 3          7          9          4          1
## CD86              1011        944        841        699        890
## MIX23               29         34         14         37         19
## PLS1                23         19         13         24         20
## PTX3               155         33        134         72        134
## GOLIM4              95         87         60         53         62
## MYNN               338        308        257        365        370
## TNFSF10           1829       2235      26922       1568       1423
## ADIPOQ               0          0          0          0          0
## SPON2              535        555        373        352        434
## S100P             3206       1743       1350       2347       3638
## WDR1              5874       5764       4190       5757       4676
## CD38               281        246        347        199        141
## PPARGC1A             0          7          2          1          1
## TMPRSS11B            0          0          0          0          0
## CSN3                 0          0          0          0          0
## ALB                  0          0          0          0          0
## CXCL8            25141      27756      39295      99946      99361
## CXCL2               12         10         64         56         25
## AREG               270         10        140         82        108
## CXCL10              22         10       1193         20         16
## CXCL13               0          0          0          2          0
## SPP1                20         29         31         13        181
## HERC6              182        189       1002        229        113
## NFKB1             1349       1009        791       1001        708
## SEC24B             568        459        370        509        353
## EGF                 28         19         16         21         12
## IL2                  3          3          0          1          1
## IL21                 0          3          1          1          0
## IL21-AS1             1          3          1          0          1
## SLC7A11             22          9         13         14          4
## IL15                87         84        111         75         64
## EDNRA                0          0          0          0          0
## TLR2              4868       2389       3816       2677       2931
## FGB                  0          0          0          0          0
## DDX60              301        320       2750        396        264
## SPCS3             2175       1950       1733       1874       1802
## TLR3                 8         12         19         15         18
## OSMR                26         19         39         27         25
## GZMK               303       1071        387       1646       1446
## GZMA               844       1235        896       1716       1344
## ANKRD55            129         26         55         63         32
## CENPK               12         25          6         97         42
## CAST              2724       3198       2061       2543       2037
## ERAP1             1272       1974       1124       1315       1006
## ERAP2             1552       1409       2366       1751        151
## TNFAIP8           1357       1568        752       1746       1096
## CSF2                 0          0          1          0          3
## IL5                  2          1          2          0          0
## IL13                 0          0          2          0          1
## IL4                  6          7          9          8          3
## CD14             12481       7501       9807       7185      10441
## CSNK1A1           1618       1615       1344       1533       1268
## PPARGC1B           174        151         83        121        104
## TNIP1             4803       4086       3311       3872       3660
## ATOX1              216        149        141        186        215
## FAXDC2             163        133        102        150         99
## IL12B                0          0          1          2          0
## MIR146A              0          1          0          1          0
## PDLIM7            1896       1759       1553       1256       1716
## SERPINB1          5576       3965       9708       3532       3575
## SSR1              2481       2084       1758       2187       2165
## CD83               456        370       2409       1064       1000
## SOX4               254        189        121        234        184
## CMAHP               93         90         80         90         58
## HLA-A            41672      43032      47586      45019      58520
## HLA-C           107225      67329      92397      84059      87157
## HLA-B           135204      92955     126018     101144     127352
## MICA               112        110        118        160        111
## LTA                 55         83         22         77         57
## TNF                358        254        380        423        388
## HLA-DRB1          4163       7194       7090       4411       8029
## HLA-DQB1           240       3980       3987        689       1989
## PPARD              411        470        157        342        292
## CCND3             5541       3845       4112       4273       3633
## VEGFA              126        161        210        216        258
## RUNX2              602        581        203        551        532
## IL17A                0          0          0          0          1
## IL17F                0          0          0          0          0
## PRDM1              612        511        760        652        604
## ATG5               487        370        320        519        398
## TRAF3IP2           214        219        109        206        168
## NCOA7              358        387       1481        369        340
## SGK1              3096       3145       3879       5397       5366
## IFNGR1            4452       2747       2129       2048       1627
## TNFAIP3           4595       2169      24118      17842      13365
## SOD2             40485      31820      58572      26143      40440
## LPAL2               12         21         14         17         13
## PLG                  0          1          2          0          1
## CCR6               115         95         54        124         79
## RAC1              3136       2332       2047       2281       2494
## ZNF316             883       1029        662        882        740
## AHR               1823       1032       1219       1342       1483
## IL6                  1          1         32         16         15
## TOMM7             2306       2242       1299       2803       2212
## CYCS               592        541        739       1046        746
## AQP1                 2          3          1          1          2
## NT5C3A             598        593       2603        530        470
## EGFR                 0          0          0          0          0
## CD36              3734       1800       1821       1851       1827
## SAMD9              999       1275       8060       1472        941
## SERPINE1             4          6         10         13          8
## CUX1              1695       1448       1270       1376       1876
## PSMC2              436        441        251        434        266
## NAMPT            64785      35240      51752      36240      45918
## HYAL4                0          1          0          0          0
## LEP                  5          8          1          4          1
## CALD1               10          2          4          8          2
## BRAF               640        639        395        655        546
## EZH2                60         91         45         60         42
## DNAJB6            1587       1354       1440       1357       1586
## CSMD1               31          7          2          1         44
## CTSB              7621       6293       5452       4905       9381
## EGR3               462        376       2011        879        640
## TNFRSF10A          194        229        118        213        143
## BNIP3L            2295       2018       2703       1812       1772
## DUSP4               47         70         73        126         81
## NRG1               150         29         25         87        100
## RPL7             10752      10980       5269      11063      10967
## IL7                  6         10         13         29          9
## GEM                  0          2          2          3          2
## MYC                895        733        284        677        438
## GPT                  1          1          3          0          4
## JAK2              1198        700       1376        828        676
## CD274              219        120       1007         81         94
## IL33                 0          1          0          0          0
## LURAP1L-AS1          0          0          0          0          0
## LURAP1L              0          0          0          0          1
## TTC39B             157        165        154        169        102
## IFNA1                0          0          0          0          0
## TEK                 13         14         12         37         25
## TRBV20OR9-2          0          0          0          0          0
## TOMM5              211        257        137        230        219
## ANXA1            10630       7868       9352       6105       6990
## ERP44             1563       1200       1507       1238       1393
## ZNF483              37         32         13         43         17
## TNFSF15              3          8          9          2          7
## TLR4              5726       3486       7468       3041       5384
## PTGS1              863        624        409        574        548
## HSPA5             6339       4338      18592       7409       7498
## FNBP1             3293       3962       2552       3537       2580
## CARD9              186        161        147        160        169
## TRAF2              122        172         74        155         91
## CLIC3              169        166         93        108        123
## IL2RA              202        155         31        103         62
## GATA3              231        477        293        632        253
## VIM              19868      16699      14247      14580      17957
## CREM               228        163        243        205        270
## DKK1                 0          0          0          0          0
## MBL2                 0          0          0          0          0
## SAR1A             1003        809        654        807        882
## PRF1              2946       2717       1605       2214       1594
## ZMIZ1             3337       2129       1465       1916       2521
## IFIT3             2497       2070     107804       2637       3322
## TALDO1            9376       8097       8591       7051       8695
## IGF2                 0          0          0          0          0
## INS-IGF2             0          0          0          0          0
## IGF2-AS              0          0          0          0          0
## INS                  0          0          0          0          0
## STIM1             1447       1401        844       1360       1118
## TRIM22            2316       2139      12338       1930       1656
## PTH                  0          0          0          0          1
## SAA1                 0          0          0          0          0
## SLC1A2               3          0          3          0          1
## FOSL1               44         19        125         78        156
## CCND1               13          4          8          8          9
## JRKL                46        108         41         85         52
## MMP7                 0          0          0          0          0
## MMP1                 2          0          3          1          0
## MMP3                 0          0          0          0          0
## CASP1             3121       2340       5848       2205       2098
## DLAT               176        222        123        234        158
## IL18               177        104         49         77         96
## CD3E              2750       3460       1807       4600       3807
## MCAM               288        231        153        226        177
## WNK1              3550       3374       1875       4062       2951
## TNFRSF1A          3341       3256       3437       2237       2800
## GAPDH            21284      17676      15229      16404      20486
## CD4               5056       4647       3238       4915       3749
## SLC2A3            8057       7376      10384       8319       9222
## CLEC4D             276        242        851        180        177
## KLRB1              595        993        339       1157       1778
## CD69              1062       1299      10880       8343       3560
## CLEC2B            1758       1474       2868       1540       1458
## OLR1                37         12          7          7          8
## ABCD2              123        190         67        292        107
## LRRK2             5003       4682       8894       4701       5065
## VDR                472        335        398        301        314
## TMBIM6           13688      12580      10878      12024      13470
## PFDN5             3692       3578       2403       3483       3803
## SP7                  0          0          0          1          1
## MUCL1                0          0          0          1          0
## CD63              3846       2888       2244       2267       3317
## SUOX               990       1106        646        935        796
## RPS26             6762       3986        575        758        828
## RPL41             7801       8916       4498       8700       8523
## IL23A               43         57         56         70         57
## DDIT3              484        509        504        661        563
## IFNG                18         37        200        189         91
## IL22                 0          2          0          0          0
## LYZ              52254     104121     125862      30869      96513
## CAPS2               10          5          2          5          5
## SYT1                 3          9          0          4          4
## BTG1             10815       8590       7913      13333      11846
## HCAR3             1560       1626       3180       3128       1915
## GJB2                 0          0          2          0          3
## GJB6                21         23          8          9         33
## TNFSF11              7          2          0          1          4
## TPT1             60558      52623      35061      58646      66369
## LMO7                98         55         30         87         49
## TNFSF13B          1717       2244      11904       1411       2159
## LAMP1             3621       2968       2560       2687       3125
## PSME2             1532       1163       2655       1330       1330
## GZMB               982       1018        829        832        889
## RPL36AL           2362       2312       1492       2660       2677
## PYGL              5421       3492       4105       3048       3483
## HIF1A             4746       2026       3373       2331       2975
## FOS              51318      38870      61969      52731      66171
## JDP2              1031        572        606        519        934
## NOXRED1              7          8          1          9          2
## SERPINA1         27328      14427      29819      17094      23425
## CDC42BPB           180        306        149        225        246
## PLA2G4D              0          0          0          0          0
## TRIM69              12         29         21         12         14
## SLC51B               0          0          0          0          0
## SMAD3              770        893        563        831        616
## CYP1A1               0          0          1          0          1
## AKAP13            4745       3966       3564       4260       3975
## MEFV              2635       2975       3648       1735       1938
## SOCS1              101         78        393        130         90
## ATXN2L            1738       2193       1165       2224       1486
## CD19                59        243         77        168        146
## ITGAL             6008       4895       3830       6501       4931
## ITGAM             5856       3733       4144       3362       5318
## ITGAX             6965       3353       6770       3060       4825
## DNAJA2             669        725        458        634        601
## SIAH1              176        155         77        138        100
## ADCY7             2066       2679       2923       2065       2242
## NOD2               597        469       1402        601       1178
## CMTM2             2040       1370       1848       1433       2439
## SF3B3              756        995        463       1317        637
## PSMD7              928        730        474        692        654
## WWOX                44         64         25         58         57
## MAF                455        753        288        695        372
## SLC7A5             294        404        294        257        583
## CXCL16            2356       1782       2164       2371       2849
## XAF1               785        627       5515        751        715
## CD68              6305       3668       5046       3422       4187
## PER1              2045        596        726        992       1625
## NOS2                 3          3          0          2          0
## TRAF4              111        133        142        145        149
## CCL2                19         13        608         15         17
## CCL5              2251       4549       2412       6977       4794
## CCL3               309        284        980        700        257
## CCR7              1419        679        558        645        514
## STAT3             4670       4538       4800       3720       2982
## SOST                 0          0          0          0          0
## ITGA2B             547        172        164        245        165
## EFCAB13             31         25         17         23         18
## NPEPPS             882        876        707        658        605
## TBX21              264        437        264        688        338
## COL1A1               0          0          2          1          0
## MRPS23             166        205        129        174        104
## MIR21                6          5          8          6          6
## RPS6KB1            429        409        237        393        332
## ACE                 30        116         18         90         39
## ERN1              1318       1550        730       1266       1293
## PRTN3               19         13          1          3          3
## PLIN5               97         87        181         57         84
## RETN               125         53         52         64         48
## CCL25                0          0          1          0          0
## ICAM1             2590       1415       2807       1589       2479
## TYK2              1642       2096       1584       1265       1149
## SMARCA4            751        797        458        799        588
## ACP5               249        272        128        226        351
## JUNB             43540      37142      43426      47541      43263
## CYP4F22            102         19         24         60         77
## JAK3              2276       1798       2642       1502       1334
## JUND              6810       5298      13026      14785      17471
## CEBPA             1099        918        445        632        986
## CEBPG              332        332        235        308        284
## ACP7                 0          2          0          0          1
## ZFP36            28362      19512      57686      60587      36305
## TGFB1             6031       5286       6535       5285       5869
## RPS19            10573      13131       5692      12367      11677
## PSG2                 0          0          0          0          0
## FUT2                 5          3          1          3          4
## NKG7              3180       3991       2639       5558       4673
## ZNF415               6         17          6          3          6
## LILRB2            6847       3699       5431       3221       4295
## LILRA5            3618       1797       5797       1129       1841
## KIR3DL1             74        174         32         91         80
## KIR3DL2             41         72         13         60         38
## SMOX                63         67         52         69         76
## BMP2                15          2          3          4          7
## GINS1                8         12          2          9          6
## PLCG1              879       1006        407        988        511
## YWHAB             6272       5643       4304       5707       5807
## PI3               4176        318       1099       1719        616
## MMP9              1300       1635       1743       1094       2417
## CD40               121        188        186        139        124
## PFDN4               58         56         22         58         55
## BMP7                 0          0          0          0          0
## RPS21             4985       5627       2651       5861       5134
## MX1                894       1023      22494        798        714
## PFKL              1155       1500        944       1362       1111
## IL17RA            4848       4600       4744       3405       3984
## UBE2L3            1149       1085        829       1028        831
## TPST2             1221       1187        870       1351       1107
## XBP1              1374       1328       1224       1168       1141
## UQCR10             607        579        403        547        553
## SEC14L2             33         29         30         37         58
## APOL6             1313       1244       9473       1387       1128
## APOL1              614        689       2813        480        602
## TYMP              3129       3970      10365       2295       3750
## BEND2               30         15         16         41         19
## PHEX                12         30          4         11          8
## TIMP1             1663       1901       1301       1107       1608
## FOXP3               73        126         34        121         60
## MSN              24991      19362      17699      23964      24816
## PGK1              9233       6819       6791       6786       8622
## LAMP2             6844       5653       5822       4881       6375
## CD40LG             171        196         90        231        154
## IRAK1             1726       1773       1169       1480       1858
## COX2             63637      53347      33759      51838      68733

4. Selection of samples

Selection of samples related to psoriatic arthritis and ankylosing spondylitis from the dataset

# sample selection
gsms <- "22222222222222222222222XXXXXXXXXXXXXXXXXXXXXXXXXXX1X0XX0001011011XXXX00XXXXXXXXXXXXXXXX0XX11022222222222222222222222222"
sml <- strsplit(gsms, split="")[[1]]

# Filter out excluded samples (marked as "X")
sel <- which(sml != "X")
sml <- sml[sel]
expr_data <- expr_data_filtered[, sel]

# group membership for samples
gs <- factor(sml)
groups <- make.names(c("PsA", "AS", "Healthy"))
levels(gs) <- groups
sample_info <- data.frame(Group = gs, row.names = colnames(expr_data))


dsa <- DESeqDataSetFromMatrix(countData=expr_data, colData=sample_info, design= ~Group)
dsb <- DESeq(dsa, test="LRT", reduced = ~ 1)  # Use LRT for all-around gene ranking
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 11 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
# extract results for top genes table
r <- results(dsb, alpha=0.05, pAdjustMethod ="fdr")

plotDispEsts(dsb, main="GSE117769 Dispersion Estimates")

# create histogram plot of p-values
hist(r$padj, breaks=seq(0, 1, length = 21), col = "grey", border = "white",
     xlab = "", ylab = "", main = "GSE117769 Frequencies of padj-values")

#Depois de filtrar quais os grupos apresentam algum genes expressos
cts <- list(c("Group",groups[1],groups[3]),
            c("Group",groups[2],groups[3]),
            c("Group",groups[2],groups[1]))  # contrasts of interest


# Wald test to obtain contrast-specific results
dsc <- DESeq(dsa, test = "Wald", sfType = "poscount")
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 9 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
r <- results (dsc, contrast=cts[[1]], alpha=0.05, pAdjustMethod = "fdr")


# Venn diagram
library(gplots)
all_res <- list()

for (ct in cts) {
  i <- length(all_res)
  r <- results(dsc, contrast=ct, alpha=0.05, pAdjustMethod = "fdr")
  all_res[[i + 1]] <- rownames(r)[!is.na(r$padj) & r$padj < 0.05 & abs(r$log2FoldChange) >= 1.0 ]
  names(all_res)[i + 1] <- paste(ct, collapse="_")
}
venn(all_res)

5. Differential gene expression analysis

# Differential gene expression analysis
df <- as.data.frame(r)
df <- na.omit(df)

topGenes <- rownames(df)
heatmapData <- expr_data[topGenes, ]

# Load the necessary libraries
library(pheatmap)
library(RColorBrewer)

# Calculate the average expression for each gene
media_dos_genes <- rowMeans(heatmapData)

# Sort the averages in descending order
media_ordenada <- sort(media_dos_genes, decreasing = TRUE)

# Get the names of the first 20 genes
top_20_genes_por_media <- names(head(media_ordenada, 20))

# Filter the original matrix to keep only the 20 selected genes
heatmapData_top20 <- heatmapData[top_20_genes_por_media, ]

# Create column annotation with groups
annotation_data <- data.frame(
  group = sample_info$Group,
  row.names = rownames(sample_info)
)

# Reorder columns by group
ordem_grupo <- order(annotation_data$group)  # Sort by group name (alphabetical)
heatmapData_top20 <- heatmapData_top20[, ordem_grupo]
annotation_data <- annotation_data[ordem_grupo, , drop = FALSE]


library(ComplexHeatmap)
library(circlize)

# Matrix of the 20 genes
mat <- heatmapData_top20

# Reschedule by line
mat_scaled <- t(scale(t(mat)))

# Create group annotation
ha_col <- HeatmapAnnotation(
  Group = annotation_data$group,
  col = list(Group = c("PsA" = "#d62728",
                       "AS" = "#1f77b4",
                       "Healthy" = "yellow"))
)

# Inverted RdBu color palette
cores <- colorRamp2(c(-2, 0, 2), rev(RColorBrewer::brewer.pal(3, "RdBu")))

# Heatmap with clustering within groups
Heatmap(
  mat_scaled,
  name = "Z-score",
  top_annotation = ha_col,
  col = cores,
  cluster_columns = TRUE,             
  cluster_column_slices = TRUE,       # << cluster within each group
  column_split = annotation_data$group, # << separate the columns by group
  cluster_rows = TRUE,
  show_column_names = FALSE,
  show_row_names = TRUE,
  column_title = "Heatmap of the 20 most highly expressed genes (average) from GSE117769",
  heatmap_legend_param = list(title = "Z-score")
)

# UMAP plot (multi-dimensional scaling)
expr_data_umap <- expr_data[rowSums(expr_data) > 0, ] # Remove rows with zero sum
u <- umap(t(expr_data_umap), n_neighbors=15, random_state=123)

plot(u$layout, main="GSE186063 UMAP", xlab="", ylab="", tcl=0.1, pch=19, col="blue")
text(u$layout, labels=colnames(expr_data_umap), cex=0.7, pos=3)

# Assuming that rownames(df) are gene symbols
gene_symbols <- rownames(df)

# Convert gene symbols to Entrez IDs
gene_entrez_ids <- bitr(gene_symbols, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)
## 'select()' returned 1:1 mapping between keys and columns
# First, convert the rownames from df into a column
df$Symbol <- rownames(df)

# Perform the join between the original table and the converted IDs
dfd <- merge(df, gene_entrez_ids, by.x = "Symbol", by.y = "SYMBOL", all.x = TRUE)

# Ensure unique symbols
dfd <- dfd[!duplicated(dfd$ENTREZID), ]

6. Comparison between peripheral blood samples from PsA patients and control samples.

# Wald test to obtain contrast-specific results
dsd <- DESeq(dsa, test = "Wald", sfType = "poscount")
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 9 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
r <- results(dsd, contrast = c("Group", groups[1], groups[3]), alpha = 0.05, pAdjustMethod = "fdr")


# Filter only significant genes
sig_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) >= 1)


# volcano plot
old.pal <- palette(c("#00BFFF", "#FF3030")) # low-hi colors
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
  plot(log2FoldChange, -log10(padj), main=paste(groups[1], "vs", groups[3]),
       xlab="log2FC", ylab="-log10(Padj)", pch=20, cex=0.5)
  text(log2FoldChange, -log10(padj), labels=rownames(r), cex=0.6, pos=4)
})
with(subset(r, padj<0.05 & abs(log2FoldChange) >= 1),
     points(log2FoldChange, -log10(padj), pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1))
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20,col=1:2)

# Plot only significant genes
#MD PLOT
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
  plot(log10(baseMean), log2FoldChange,
       main=paste(groups[1], "vs", groups[3]),
       xlab="log10(mean of normalized counts)", ylab="log2FoldChange",
       pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1)
  text(log10(baseMean), log2FoldChange, labels=rownames(sig_genes), cex=0.6, pos=4)
})
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20, col=1:2)
abline(h=0)

palette(old.pal) # restaurar paleta

# Add the gene symbols to the points on the graph.

library(ggplot2)
library(ggrepel)

plotVolcano <- function(res, title = "Volcano Plot") {
  res$group <- "NS"
  res$group[res$padj < 0.05 & res$log2FoldChange > 1] <- "Up"
  res$group[res$padj < 0.05 & res$log2FoldChange < -1] <- "Down"
  
  res$label <- ifelse(res$group != "NS", rownames(res), NA)
  
  ggplot(res, aes(x = log2FoldChange, y = -log10(padj), color = group)) +
    geom_point(alpha = 0.7, size = 2) +
    geom_hline(yintercept = -log10(0.05), linetype = "dashed") +
    geom_vline(xintercept = c(-1, 1), linetype = "dashed") +
    scale_color_manual(values = c("Up" = "firebrick", "Down" = "dodgerblue", "NS" = "grey80")) +
    ggrepel::geom_text_repel(aes(label = label), size = 3, max.overlaps = Inf) +
    theme_minimal() +
    labs(title = title, x = "log2 Fold Change", y = "-log10 adjusted p-value", color = "Regulation")
}

# Example of function usage
plotVolcano(r, paste(groups[1], "vs", groups[3]))
## Warning: Removed 13 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 422 rows containing missing values or values outside the scale range
## (`geom_text_repel()`).

# Genes upregulated
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange >= 1))

# Genes downregulated
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange <= -1))

# All DEGs with |log2FC| > 2
de_genes <- c(up_genes, down_genes)

# Display gene symbols before conversion
expr_datasa <- as.data.frame(expr_data[rownames(expr_data) %in% de_genes, ])

# Convert expression data to long format for ggplot2
expr_datas <- as.data.frame(expr_datasa)
expr_datas$Gene <- rownames(expr_datas)
expr_datas <- pivot_longer(expr_datas, cols = -Gene, names_to = "Sample", values_to = "Expression")
expr_datas <- merge(expr_datas, pheno_data, by.x = "Sample", by.y = "geo_accession")

# Check column names and a sample of the data
expresse <- r[order(r$padj)[1:429], ]
expresse <- merge(as.data.frame(expresse), expr_datasa, by = 0, sort = F)


library(dplyr)
library(tibble)
library(clusterProfiler)
library(ggplot2)

r_df <- as.data.frame(r)

# This ensures that gene names are preserved
r_df_com_genes <- r_df %>%
  rownames_to_column(var = "Gene") 

# --- Now, the rest of your code works perfectly ---
top30_fc <- r_df_com_genes %>%
  # O 'filter' também pode ser conflitante, é bom usar o prefixo
  dplyr::filter(padj < 0.05 & abs(log2FoldChange) > 1) %>%
  dplyr::arrange(desc(abs(log2FoldChange))) %>%
  # Esta é a correção principal:
  dplyr::slice(1:30) %>%
  dplyr::mutate(
    Regulation = case_when(
      log2FoldChange > 1 ~ "Upregulated",
      log2FoldChange < -1 ~ "Downregulated"
    )
  )


# Graph with positive and negative bars (your code here is perfect)
ggplot(top30_fc, aes(x = reorder(Gene, log2FoldChange), y = log2FoldChange, fill = Regulation)) +
  geom_col() +
  coord_flip() + # Coloca os genes no eixo Y
  scale_fill_manual(values = c("Upregulated" = "steelblue", "Downregulated" = "tomato")) +
  scale_y_continuous(breaks = seq(-8, 4, by = 1)) + # Ajuste os limites se necessário
  theme_bw() +
  labs(
    title = "The 30 most prominent DEGs between PsA and Healthy (GSE117769)",
    x = "Gene",
    y = "log2 Fold Change",
    fill = "Regulation"
  ) + 
  theme(
    axis.text.y = element_text(color = "black", face = "bold", size = 9)
  )

# --- Select the 20 MOST overexpressed genes ---
up_20genes <- expresse %>%
  filter(padj < 0.05 & log2FoldChange > 1) %>%
  arrange(desc(log2FoldChange)) %>% 
  head(20) %>%
  pull(Row.names)

# --- Filters expression data ---
expr_datas_filtrado_up <- expr_datas %>%
  filter(`characteristics_ch1.6` %in% c("phenotype: Psoriatic arthritis", "phenotype: Healthy")) %>%
  filter(Gene %in% up_20genes)

# --- Calculate the average per gene and per group ---
expr_datasa_up <- expr_datas_filtrado_up %>%
  group_by(Gene, `characteristics_ch1.6`) %>%
  summarise(
    mean_expression = mean(Expression, na.rm = TRUE),
    sd_expression = sd(Expression, na.rm = TRUE),
    .groups = 'drop'
  )

# --- Preparation for the chart ---
dados_para_plotar_up <- expr_datasa_up %>%
  filter(characteristics_ch1.6 == "phenotype: Psoriatic arthritis")

# --- Graph Generation ---
ggplot(dados_para_plotar_up, aes(x = mean_expression, y = reorder(Gene, mean_expression))) +
  geom_col(fill = "steelblue", color = "black", width = 0.7) +
  labs(
    title = "Average Expression of the Main Upregulated Genes in Psoriatic arthritis", # Título mais claro
    subtitle = "For PsA vs Healthy (GSE117769)",
    x = "Average Expression in the Group 'PsA'", # Rótulo do eixo mais claro
    y = "Gene"
  ) +
  theme_minimal(base_size = 14) +
  theme(
    panel.grid.major.y = element_blank(),
    axis.text.y = element_text(size = 12)
  )

# --- Selects the 20 MOST under-expressed genes ---
down_20genes <- expresse %>%
  filter(padj < 0.05 & log2FoldChange < -1) %>%
  arrange(log2FoldChange) %>% # <-- Sort from most negative to least negative
  head(20) %>%
  pull(Row.names)

# --- Filters expression data for genes and groups of interest ---
expr_datas_filtrado_down <- expr_datas %>%
  filter(`characteristics_ch1.6` %in% c("phenotype: Psoriatic arthritis", "phenotype: Healthy")) %>%
  filter(Gene %in% down_20genes)

# --- Calculate the average per gene and per group ---
expr_datasa_down <- expr_datas_filtrado_down %>%
  group_by(Gene, `characteristics_ch1.6`) %>%
  summarise(
    mean_expression = mean(Expression, na.rm = TRUE),
    .groups = 'drop'
  )

# --- Preparation for the chart ---'
dados_para_plotar <- expr_datasa_down %>%
  filter(characteristics_ch1.6 == "phenotype: Psoriatic arthritis")

# --- Graph Generation ---
ggplot(dados_para_plotar, aes(x = mean_expression, y = reorder(Gene, -mean_expression))) +
  geom_col(fill = "red", color = "black", width = 0.7) +
  labs(
    title = "Average Expression of the Main Downregulated Genes in Psoriatic arthritis", # Título mais claro
    subtitle = "For PsA vs Healthy (GSE117769)",
    x = "Average Expression in the Group 'PsA'", # Rótulo do eixo mais claro
    y = "Gene"
  ) +
  theme_minimal(base_size = 14) +
  theme(
    panel.grid.major.y = element_blank(),
    axis.text.y = element_text(size = 12)
  )

# --- Create 'count_matrix' ---
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange > 1))
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange < -1))
genes_interesse <- c(up_genes, down_genes)

expr_filtrado <- expr_datas %>%
  filter(`characteristics_ch1.6` %in% c("phenotype: Psoriatic arthritis", "phenotype: Healthy")) %>%
  filter(Gene %in% genes_interesse)

matriz_contagem <- expr_filtrado %>%
  select(Gene, Sample, Expression) %>%
  pivot_wider(names_from = Sample, values_from = Expression, values_fill = 0) %>%
  column_to_rownames(var = "Gene")


# Filter your original “sample_info” object to keep only the samples that are in your final matrix.
# This ensures that the annotation corresponds exactly to the heatmap data.
sample_info_filtrado <- subset(sample_info, rownames(sample_info) %in% colnames(matriz_contagem))


# Select the 20 most highly expressed genes 
media_dos_genes <- rowMeans(matriz_contagem)
media_ordenada <- sort(media_dos_genes, decreasing = TRUE)
top_20_genes_por_media <- names(head(media_ordenada, 20))
heatmapData_top20 <- as.matrix(matriz_contagem[top_20_genes_por_media, ])


# Create the annotation for the heatmap from the already filtered information.
annotation_data <- data.frame(
  Group = sample_info_filtrado$Group,
  row.names = rownames(sample_info_filtrado)
)

# Ensure that the order of the columns in the heatmap and annotation is the same.
heatmapData_top20 <- heatmapData_top20[, rownames(annotation_data)]


# --- Heatmap generation with ComplexHeatmap ---

library(ComplexHeatmap)
library(circlize)
library(RColorBrewer)

# Rescale data by row (Z-score)
mat_scaled <- t(scale(t(heatmapData_top20)))

# Create the column annotation
ha_col <- HeatmapAnnotation(
  Group = annotation_data$Group,
  col = list(Group = c("PsA" = "red", "Healthy" = "yellow"))
)

# Define the colour palette
cores <- colorRamp2(c(-2, 0, 2), rev(RColorBrewer::brewer.pal(3, "RdBu")))

# Generate the heatmap
Heatmap(
  mat_scaled,
  name = "Z-score",
  top_annotation = ha_col,
  col = cores,
  
  # Divide the columns into groups for clearer viewing
  column_split = annotation_data$Group,
  
  cluster_rows = TRUE,
  cluster_columns = TRUE, # Cluster within each divided group
  
  show_column_names = FALSE,
  show_row_names = TRUE,
  column_title = "Heatmap of the most highly expressed DEGs (PsA vs. Healthy GSE117769)",
  heatmap_legend_param = list(title = "Z-score")
)

# Filter differentially expressed genes
de_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) > 1)

# Create a data frame from de_genes
de_genes <- data.frame(de_genes)

# Suppose your dataframe is called df and you want to select columns ‘column1’, “column2” and ‘column3’.
de_genes <- de_genes %>% select(log2FoldChange, padj)

# Assuming that rownames(df) are gene symbols
gene_symbols <- rownames(de_genes)

# Convert gene symbols to Entrez IDs
gene_entrez_ids <- bitr(gene_symbols, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)
## 'select()' returned 1:1 mapping between keys and columns
# First, convert the rownames from df into a column
de_genes$Symbol <- rownames(de_genes)

# Join the original table and the converted IDs
de_genes <- merge(de_genes, gene_entrez_ids, by.x = "Symbol", by.y = "SYMBOL", all.x = TRUE)

# Ensure unique symbols
de_genes <- de_genes[!duplicated(de_genes$ENTREZID), ]

# View the first results to verify the addition of the IDs
de_genes <- de_genes %>% 
  filter(Symbol %in% rownames(matriz_contagem))
                               

BiocManager::install("GOSemSim")
## 'getOption("repos")' replaces Bioconductor standard repositories, see
## 'help("repositories", package = "BiocManager")' for details.
## Replacement repositories:
##     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
## Bioconductor version 3.20 (BiocManager 1.30.26), R 4.4.1 (2024-06-14)
## Installing package(s) 'GOSemSim'
## Warning in install.packages(...): installation of package 'GOSemSim' had
## non-zero exit status
## Installation paths not writeable, unable to update packages
##   path: /usr/local/lib/R/library
##   packages:
##     boot, class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv,
##     nlme, nnet, rpart, spatial, survival
##   path: /usr/local/lib/R/site-library
##   packages:
##     annotate, AnnotationDbi, ape, aplot, askpass, BH, Biobase, BiocFileCache,
##     BiocGenerics, BiocManager, BiocParallel, BiocVersion, biomaRt, Biostrings,
##     bit, bit64, bitops, Boruta, broom, bslib, C50, car, caret, checkmate, chk,
##     classInt, cli, clock, clue, clusterProfiler, colorspace, commonmark,
##     ComplexHeatmap, corrplot, cowplot, cpp11, credentials, crosstalk, Cubist,
##     cutpointr, dbplyr, dbscan, DelayedArray, DEoptimR, Deriv, DESeq2, devtools,
##     DiceKriging, diffobj, doBy, docopt, DOSE, dotCall64, downloader, DT,
##     dtplyr, edgeR, enrichplot, entropy, evaluate, fastDummies, fastmatch,
##     fgsea, fitdistrplus, fontawesome, forcats, fs, future, future.apply,
##     gargle, GDCRNATools, genefilter, generics, GenomeInfoDb, GenomeInfoDbData,
##     GenomicDataCommons, GenomicRanges, gert, ggforce, ggfun, ggnewscale,
##     ggplot2, ggplotify, ggpubr, ggraph, ggridges, ggsci, ggtree, gh, gld,
##     glmnet, globals, glue, GO.db, googledrive, googlesheets4, GOSemSim, gower,
##     GPArotation, gplots, graph, graphlayouts, gtable, hardhat, haven, HDO.db,
##     here, hms, httpuv, httr2, IRanges, jpeg, jsonlite, KEGGgraph, KEGGREST,
##     keras, KMsurv, knitr, labelled, later, lava, lavaan, lgr, limma, littler,
##     lme4, lmom, locfit, lubridate, magrittr, markdown, MatchIt, MatrixGenerics,
##     MatrixModels, matrixStats, maxstat, mice, mime, miniUI, mlbench, mlr3,
##     mlr3learners, mlr3measures, mlr3misc, mlr3pipelines, modeltools, multcomp,
##     mvtnorm, networkD3, nloptr, org.Hs.eg.db, party, partykit, patchwork,
##     pathview, pbapply, pbkrtest, pillar, pkgbuild, pkgdown, pkgload, plotly,
##     pROC, processx, prodlim, progressr, PRROC, ps, psych, purrr, quantmod,
##     quantreg, questionr, qvalue, R.cache, R.oo, R.utils, R6, ragg, ranger,
##     Rcpp, RcppArmadillo, RcppTOML, RCurl, readxl, recipes, reshape, rgl,
##     Rgraphviz, rlang, rmarkdown, robustbase, roxygen2, rprojroot, rsq, rstatix,
##     rstudioapi, rversions, rvest, S4Arrays, S4Vectors, sass, scales,
##     scatterpie, sctransform, sessioninfo, Seurat, SeuratObject, shadowtext,
##     shiny, sp, spam, SparseArray, spatstat.data, spatstat.explore,
##     spatstat.geom, spatstat.random, spatstat.univar, spatstat.utils, statmod,
##     stringi, stringr, styler, SummarizedExperiment, survminer, sva, svglite,
##     sys, systemfonts, TCGAbiolinks, TCGAbiolinksGUI.data, tensor, tensorflow,
##     testthat, textshaping, tfruns, TH.data, tibble, timeDate, tinytex, treeio,
##     tzdb, UCSC.utils, usethis, utf8, uwot, VIM, vroom, waldo, withr, xgboost,
##     XML, xml2, xts, XVector, yulab.utils, zeallot, zip, zlibbioc, zoo
## Old packages: 'curl', 'data.table', 'Hmisc', 'igraph', 'openssl', 'parallelly',
##   'promises', 'reticulate', 'RSQLite', 'xfun'
library(GOSemSim)
  
BiocManager::install("enrichplot")
## 'getOption("repos")' replaces Bioconductor standard repositories, see
## 'help("repositories", package = "BiocManager")' for details.
## Replacement repositories:
##     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
## Bioconductor version 3.20 (BiocManager 1.30.26), R 4.4.1 (2024-06-14)
## Installing package(s) 'enrichplot'
## also installing the dependencies 'DOSE', 'GOSemSim'
## Warning in install.packages(...): installation of package 'GOSemSim' had
## non-zero exit status
## Warning in install.packages(...): installation of package 'DOSE' had non-zero
## exit status
## Warning in install.packages(...): installation of package 'enrichplot' had
## non-zero exit status
## Installation paths not writeable, unable to update packages
##   path: /usr/local/lib/R/library
##   packages:
##     boot, class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv,
##     nlme, nnet, rpart, spatial, survival
##   path: /usr/local/lib/R/site-library
##   packages:
##     annotate, AnnotationDbi, ape, aplot, askpass, BH, Biobase, BiocFileCache,
##     BiocGenerics, BiocManager, BiocParallel, BiocVersion, biomaRt, Biostrings,
##     bit, bit64, bitops, Boruta, broom, bslib, C50, car, caret, checkmate, chk,
##     classInt, cli, clock, clue, clusterProfiler, colorspace, commonmark,
##     ComplexHeatmap, corrplot, cowplot, cpp11, credentials, crosstalk, Cubist,
##     cutpointr, dbplyr, dbscan, DelayedArray, DEoptimR, Deriv, DESeq2, devtools,
##     DiceKriging, diffobj, doBy, docopt, DOSE, dotCall64, downloader, DT,
##     dtplyr, edgeR, enrichplot, entropy, evaluate, fastDummies, fastmatch,
##     fgsea, fitdistrplus, fontawesome, forcats, fs, future, future.apply,
##     gargle, GDCRNATools, genefilter, generics, GenomeInfoDb, GenomeInfoDbData,
##     GenomicDataCommons, GenomicRanges, gert, ggforce, ggfun, ggnewscale,
##     ggplot2, ggplotify, ggpubr, ggraph, ggridges, ggsci, ggtree, gh, gld,
##     glmnet, globals, glue, GO.db, googledrive, googlesheets4, GOSemSim, gower,
##     GPArotation, gplots, graph, graphlayouts, gtable, hardhat, haven, HDO.db,
##     here, hms, httpuv, httr2, IRanges, jpeg, jsonlite, KEGGgraph, KEGGREST,
##     keras, KMsurv, knitr, labelled, later, lava, lavaan, lgr, limma, littler,
##     lme4, lmom, locfit, lubridate, magrittr, markdown, MatchIt, MatrixGenerics,
##     MatrixModels, matrixStats, maxstat, mice, mime, miniUI, mlbench, mlr3,
##     mlr3learners, mlr3measures, mlr3misc, mlr3pipelines, modeltools, multcomp,
##     mvtnorm, networkD3, nloptr, org.Hs.eg.db, party, partykit, patchwork,
##     pathview, pbapply, pbkrtest, pillar, pkgbuild, pkgdown, pkgload, plotly,
##     pROC, processx, prodlim, progressr, PRROC, ps, psych, purrr, quantmod,
##     quantreg, questionr, qvalue, R.cache, R.oo, R.utils, R6, ragg, ranger,
##     Rcpp, RcppArmadillo, RcppTOML, RCurl, readxl, recipes, reshape, rgl,
##     Rgraphviz, rlang, rmarkdown, robustbase, roxygen2, rprojroot, rsq, rstatix,
##     rstudioapi, rversions, rvest, S4Arrays, S4Vectors, sass, scales,
##     scatterpie, sctransform, sessioninfo, Seurat, SeuratObject, shadowtext,
##     shiny, sp, spam, SparseArray, spatstat.data, spatstat.explore,
##     spatstat.geom, spatstat.random, spatstat.univar, spatstat.utils, statmod,
##     stringi, stringr, styler, SummarizedExperiment, survminer, sva, svglite,
##     sys, systemfonts, TCGAbiolinks, TCGAbiolinksGUI.data, tensor, tensorflow,
##     testthat, textshaping, tfruns, TH.data, tibble, timeDate, tinytex, treeio,
##     tzdb, UCSC.utils, usethis, utf8, uwot, VIM, vroom, waldo, withr, xgboost,
##     XML, xml2, xts, XVector, yulab.utils, zeallot, zip, zlibbioc, zoo
## Old packages: 'curl', 'data.table', 'Hmisc', 'igraph', 'openssl', 'parallelly',
##   'promises', 'reticulate', 'RSQLite', 'xfun'
library(enrichplot)
BiocManager::install("STRINGdb")
## 'getOption("repos")' replaces Bioconductor standard repositories, see
## 'help("repositories", package = "BiocManager")' for details.
## Replacement repositories:
##     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
## Bioconductor version 3.20 (BiocManager 1.30.26), R 4.4.1 (2024-06-14)
## Warning: package(s) not installed when version(s) same as or greater than current; use
##   `force = TRUE` to re-install: 'STRINGdb'
## Installation paths not writeable, unable to update packages
##   path: /usr/local/lib/R/library
##   packages:
##     boot, class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv,
##     nlme, nnet, rpart, spatial, survival
##   path: /usr/local/lib/R/site-library
##   packages:
##     annotate, AnnotationDbi, ape, aplot, askpass, BH, Biobase, BiocFileCache,
##     BiocGenerics, BiocManager, BiocParallel, BiocVersion, biomaRt, Biostrings,
##     bit, bit64, bitops, Boruta, broom, bslib, C50, car, caret, checkmate, chk,
##     classInt, cli, clock, clue, clusterProfiler, colorspace, commonmark,
##     ComplexHeatmap, corrplot, cowplot, cpp11, credentials, crosstalk, Cubist,
##     cutpointr, dbplyr, dbscan, DelayedArray, DEoptimR, Deriv, DESeq2, devtools,
##     DiceKriging, diffobj, doBy, docopt, DOSE, dotCall64, downloader, DT,
##     dtplyr, edgeR, enrichplot, entropy, evaluate, fastDummies, fastmatch,
##     fgsea, fitdistrplus, fontawesome, forcats, fs, future, future.apply,
##     gargle, GDCRNATools, genefilter, generics, GenomeInfoDb, GenomeInfoDbData,
##     GenomicDataCommons, GenomicRanges, gert, ggforce, ggfun, ggnewscale,
##     ggplot2, ggplotify, ggpubr, ggraph, ggridges, ggsci, ggtree, gh, gld,
##     glmnet, globals, glue, GO.db, googledrive, googlesheets4, GOSemSim, gower,
##     GPArotation, gplots, graph, graphlayouts, gtable, hardhat, haven, HDO.db,
##     here, hms, httpuv, httr2, IRanges, jpeg, jsonlite, KEGGgraph, KEGGREST,
##     keras, KMsurv, knitr, labelled, later, lava, lavaan, lgr, limma, littler,
##     lme4, lmom, locfit, lubridate, magrittr, markdown, MatchIt, MatrixGenerics,
##     MatrixModels, matrixStats, maxstat, mice, mime, miniUI, mlbench, mlr3,
##     mlr3learners, mlr3measures, mlr3misc, mlr3pipelines, modeltools, multcomp,
##     mvtnorm, networkD3, nloptr, org.Hs.eg.db, party, partykit, patchwork,
##     pathview, pbapply, pbkrtest, pillar, pkgbuild, pkgdown, pkgload, plotly,
##     pROC, processx, prodlim, progressr, PRROC, ps, psych, purrr, quantmod,
##     quantreg, questionr, qvalue, R.cache, R.oo, R.utils, R6, ragg, ranger,
##     Rcpp, RcppArmadillo, RcppTOML, RCurl, readxl, recipes, reshape, rgl,
##     Rgraphviz, rlang, rmarkdown, robustbase, roxygen2, rprojroot, rsq, rstatix,
##     rstudioapi, rversions, rvest, S4Arrays, S4Vectors, sass, scales,
##     scatterpie, sctransform, sessioninfo, Seurat, SeuratObject, shadowtext,
##     shiny, sp, spam, SparseArray, spatstat.data, spatstat.explore,
##     spatstat.geom, spatstat.random, spatstat.univar, spatstat.utils, statmod,
##     stringi, stringr, styler, SummarizedExperiment, survminer, sva, svglite,
##     sys, systemfonts, TCGAbiolinks, TCGAbiolinksGUI.data, tensor, tensorflow,
##     testthat, textshaping, tfruns, TH.data, tibble, timeDate, tinytex, treeio,
##     tzdb, UCSC.utils, usethis, utf8, uwot, VIM, vroom, waldo, withr, xgboost,
##     XML, xml2, xts, XVector, yulab.utils, zeallot, zip, zlibbioc, zoo
## Old packages: 'curl', 'data.table', 'Hmisc', 'igraph', 'openssl', 'parallelly',
##   'promises', 'reticulate', 'RSQLite', 'xfun'
library(STRINGdb)

#Alternative Workflow with STRINGdb Integration in R
# Initialise the STRINGdb object for a specific organism
string_db <- STRINGdb$new(version = "12", species = 9606, score_threshold = 400, input_directory = "")

options(timeout = 600)  # increases to 10 minutes

# Gene mapping using STRINGdb
mapped_genes <- string_db$map(de_genes, "Symbol", removeUnmappedRows = TRUE)

# Recover interactions for mapped genes
interactions <- string_db$get_interactions(mapped_genes$STRING_id)

# Visualise the network using igraph or other visualisation tools
library(igraph)
## 
## Attaching package: 'igraph'
## The following object is masked from 'package:tibble':
## 
##     as_data_frame
## The following objects are masked from 'package:rtracklayer':
## 
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## 
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## 
##     crossing
## The following objects are masked from 'package:dplyr':
## 
##     as_data_frame, groups, union
## The following object is masked from 'package:GenomicRanges':
## 
##     union
## The following object is masked from 'package:IRanges':
## 
##     union
## The following object is masked from 'package:S4Vectors':
## 
##     union
## The following objects are masked from 'package:BiocGenerics':
## 
##     normalize, path, union
## The following objects are masked from 'package:stats':
## 
##     decompose, spectrum
## The following object is masked from 'package:base':
## 
##     union
g <- graph_from_data_frame(interactions, directed=FALSE)
plot(g)

# Detect clusters (e.g. Louvain)
clusters <- cluster_louvain(g)

# Plot with colours by cluster
plot(g, vertex.color=clusters$membership)

# Perform GO enrichment analysis
# Biological Process
# Ensure you have the packages installed
library(clusterProfiler)
library(org.Hs.eg.db)
library(ggplot2)
library(dplyr) # For data manipulation


# Biological Process
enrich_result <- enrichGO(gene = mapped_genes$Symbol,
                          OrgDb = org.Hs.eg.db,
                          keyType = "SYMBOL",
                          ont = "BP", # Biological Ontology. It can be ‘BP’, “MF”, or ‘CC’
                          pAdjustMethod = "BH", # Benjamini-Hochberg (BH) is the same as FDR.
                          pvalueCutoff = 0.05,
                          qvalueCutoff = 0.2)


if (is.null(enrich_result) || nrow(as.data.frame(enrich_result)) == 0) {
  print("No significantly enriched GO terms were found with the provided criteria.")
} else {
  plot_data <- as.data.frame(enrich_result) %>%
    arrange(p.adjust) %>%
    head(15) # Display the 15 most significant terms
  
  # Create a numeric column for the Y axis to use with geom_segment
  # The order of the terms on the Y axis is important.
  plot_data$y_pos <- rev(seq_along(plot_data$Description)) # To sort from top to bottom
  
  ggplot(plot_data, aes(x = Count, y = y_pos)) + # Use y_pos for the Y axis
    # Add geom_segment for the ‘threads’
    # It starts at x=0 (or a small value) and goes up to the Count of the term.
    geom_segment(aes(x = 0, xend = Count, y = y_pos, yend = y_pos),
                 color = "gray", linewidth = 0.5) +
    geom_point(aes(size = Count, color = p.adjust), alpha = 0.8) +
    scale_color_gradientn(
      colors = c("darkblue", "steelblue", "lightblue", "lightgreen", "yellow", "orange", "darkred"),
      name = "FDR",
      trans = "log10",
      breaks = scales::trans_breaks("log10", function(x) 10^x),
      labels = scales::trans_format("log10", scales::math_format(10^.x))
    ) +
    scale_size_area(max_size = 15, name = "Contagem de Genes") +
    # Map labels back to GO descriptions
    scale_y_continuous(breaks = plot_data$y_pos, labels = plot_data$Description) +
    labs(
      title = "GO Enrichment Analysis (Biological Processes)",
      x = "Genes Counting",
      y = "GO Terms (Biological Processes)"
    ) +
    theme_minimal() +
    theme(
      axis.text.y = element_text(size = 12, face = "bold"),
      axis.title = element_text(size = 14, face = "bold"),
      plot.title = element_text(size = 16, face = "bold", hjust = 0.5),
      legend.position = "right",
      legend.title = element_text(size = 12, face = "bold"),
      legend.text = element_text(size = 10),
      panel.grid.major.y = element_blank(), # Remove the default horizontal grid lines
      panel.grid.minor = element_blank(),
      panel.border = element_rect(colour = "black", fill=NA, linewidth=1)
    )
}

barplot(enrich_result, showCategory = 10, title= "GO Enrichment Analysis")
## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?
## Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
## ℹ Please use tidy evaluation idioms with `aes()`.
## ℹ See also `vignette("ggplot2-in-packages")` for more information.
## ℹ The deprecated feature was likely used in the enrichplot package.
##   Please report the issue at
##   <https://github.com/GuangchuangYu/enrichplot/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

# Network graph of enriched terms
cnetplot(enrich_result, showCategory = 10)
## Warning: `aes_()` was deprecated in ggplot2 3.0.0.
## ℹ Please use tidy evaluation idioms with `aes()`
## ℹ The deprecated feature was likely used in the enrichplot package.
##   Please report the issue at
##   <https://github.com/GuangchuangYu/enrichplot/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

# Heatmap
heatplot(enrich_result, showCategory = 10)

# Perform KEGG enrichment analysis
ekegg <- enrichKEGG(gene = mapped_genes$ENTREZID, organism = "hsa", pAdjustMethod = "BH", qvalueCutoff = 0.05)
## Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
## Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
# Generate GO/STRING style bubble chart
if (is.null(ekegg) || nrow(as.data.frame(ekegg)) == 0) {
  print("No significantly enriched KEGG pathways were found with the criteria provided.")
} else {
  plot_data_kegg <- as.data.frame(ekegg) %>%
    arrange(p.adjust) %>% # Sort by p.adjust (FDR)
    head(15) # Selects the 15 most significant pathways to plot

  # Creates a numerical position for the terms on the Y-axis, to control the order and lines
  plot_data_kegg$y_pos <- rev(seq_along(plot_data_kegg$Description)) # reverse to the most significant at the top
  
  # Starting to build the graph with ggplot2
  ggplot(plot_data_kegg, aes(x = Count, y = y_pos)) +
    # Adds the connection lines (wires) from the Y-axis to the bubble.
    geom_segment(aes(x = 0, xend = Count, y = y_pos, yend = y_pos),
                 color = "gray80", linewidth = 0.6) + # Softer colour for the lines
    # Add the bubbles
    geom_point(aes(size = Count, color = p.adjust), alpha = 0.9) +
    # Colour scale configuration for FDR (p.adjust)
    scale_color_gradientn(
      colors = c("darkblue", "steelblue", "lightblue", "lightgreen", "yellow", "orange", "darkred"),
      name = "FDR",
      trans = "log10", # Use logarithmic scale for FDR
      breaks = scales::trans_breaks("log10", function(x) 10^x), # Breaks in scientific notation captions
      labels = scales::trans_format("log10", scales::math_format(10^.x)), # Scientific notation format
      limits = c(min(plot_data_kegg$p.adjust), max(plot_data_kegg$p.adjust)) # Sets limits for data
    ) +
    # Size scale configuration for Gene Counting
    scale_size_area(
      max_size = 18, # Maximum bubble size
      name = "Gene count", # Caption title size
      breaks = unique(round(quantile(plot_data_kegg$Count, probs = c(0.25, 0.5, 0.75, 1.0)))), # Suggests reasonable breaks
      labels = unique(round(quantile(plot_data_kegg$Count, probs = c(0.25, 0.5, 0.75, 1.0))))
    ) +
    # Maps the Y-axis labels back to the KEGG pathway descriptions
    scale_y_continuous(
      breaks = plot_data_kegg$y_pos,
      labels = plot_data_kegg$Description
    ) +
    # Labels and Chart Title
    labs(
      title = "KEGG Pathway Enrichment Analysis",
      x = "Gene count", # X-axis is now Gene Count
      y = "KEGG Pathway" # Y-axis is the name of the pathway
    ) +
    # Chart Theme and Style
    theme_minimal() +
    theme(
      axis.text.y = element_text(size = 12, face = "bold"), # KEGG terms in bold and larger font
      axis.title = element_text(size = 14, face = "bold"), # Axis titles
      plot.title = element_text(size = 16, face = "bold", hjust = 0.5), # Centred title
      legend.position = "right", # Position of subtitles
      legend.title = element_text(size = 12, face = "bold"),
      legend.text = element_text(size = 10),
      panel.grid.major.y = element_blank(), # Remove standard horizontal grid lines
      panel.grid.minor = element_blank(), # Remove minor grid liness
      panel.border = element_rect(colour = "black", fill=NA, linewidth=1.2) # Black border around the plot
    )
} 

barplot(ekegg, showCategory = 10, title = "KEGG Enrichment Analysis")
## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?

# Network graph of enriched terms
cnetplot(ekegg, showCategory = 10)

# Heatmap
heatplot(ekegg, showCategory = 10)

7.Transcription factors in the analysis between PsA vs Healthy

# Load the necessary packages
library(GenomicFeatures)
## 
## Attaching package: 'GenomicFeatures'
## The following object is masked from 'package:topGO':
## 
##     genes
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(org.Hs.eg.db)
library(JASPAR2020)
library(TFBSTools)
library(SummarizedExperiment)
library(motifmatchr)

# Load the TxDb database
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene

# Extraction of exons by gene
exons_by_gene <- exonsBy(txdb, by = "gene")

# Obtain the coordinates of the genes (taking the first and last positions of the exons)
genes_info <- range(exons_by_gene)

# Obtain transcription information
transcripts_info <- transcripts(txdb)

# Map genes of interest to Entrez IDs (replace “de_genes” with the actual list of genes)
gene_entrez <- mapIds(org.Hs.eg.db, keys = mapped_genes$Symbol, column = "ENTREZID", keytype = "SYMBOL", multiVals = "first")
## 'select()' returned 1:1 mapping between keys and columns
# Filter the genes of interest
promoters_info <- subset(genes_info, names(genes_info) %in% gene_entrez)

# Define promoter regions (2 kb upstream of TSS)
promoters <- promoters(promoters_info, upstream = 2000, downstream = 0)

# Filter the main chromosomes
promoters <- keepStandardChromosomes(promoters, pruning.mode = "coarse")

# Remove any regions that exceed the limits of the chromosomes.
promoters <- trim(promoters)

# Convert CompressedGRangesList promoters to GRanges
promoters_gr <- unlist(promoters)

# Load the JASPAR grounds database
motifs <- getMatrixSet(JASPAR2020, opts = list(species = "Homo sapiens"))

# Create a data frame with the IDs of the reasons and their names (TFs)
motif_info <- data.frame(
  motif_id = names(motifs),
  tf_name = sapply(motifs, function(x) x@name),
  stringsAsFactors = FALSE
)

# Enriching motifs in promoting regions
motifHits <- matchMotifs(motifs, promoters_gr, genome = BSgenome.Hsapiens.UCSC.hg38)

# Count the number of occurrences of the reasons in each promoting region.
motif_counts <- countOverlaps(promoters_gr, motifHits)

# Add counts to GRanges with promoting regions
promoters_gr$motif_counts <- motif_counts

# Summary of motif counts
summary(promoters_gr$motif_counts)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##     0.0     0.0     0.5     0.5     1.0     1.0
# Obtain the names of the motifs and TFs
motif_names <- names(motifHits)

# Extract the reason table from the RangedSummarizedExperiment object
motif_data <- assays(motifHits)[[1]] # Assuming that the table of reasons is in the first list of assays

# Obtain information about TFs
# The names of TFs may be in the colnames or in associated metadata
tf_names <- colnames(motif_data)  

# Add the reason count if available
motif_counts <- rowSums(motif_data) 

# Check the dimensions of the motif_data object
dim(motif_data) # Number of rows and columns
## [1]   6 633
# Check the length of tf_names and motif_counts
tf_names_length <- length(tf_names)
motif_counts_length <- length(motif_counts)

# Print the lengths for diagnosis
cat("Length of tf_names:", tf_names_length, "\n")
## Length of tf_names: 633
cat("Length of motif_counts:", motif_counts_length, "\n")
## Length of motif_counts: 6
# Verify that the dimensions of motif_data correspond to the number of TFs and motifs
motif_data_dims <- dim(motif_data)
cat("Dimensions of motif_data (rows, columns):", motif_data_dims, "\n")
## Dimensions of motif_data (rows, columns): 6 633
# Check whether the number of reasons is greater or lesser
if (tf_names_length > motif_counts_length) {
  # Check additional columns
  tf_names <- tf_names[1:motif_counts_length] # Adjust to the length of motif_counts
} else {
  # Adjust motif_counts to match tf_names
  motif_counts <- motif_counts[1:tf_names_length]
}

# Now, create the data frame with adjusted lengths
motif_summary <- data.frame(
  tf_name = tf_names,
  motif_count = motif_counts
)

# Check the correspondence between TF names and the columns in motif_data
all(tf_names %in% colnames(motif_data)) # Should return TRUE if all TF names are present
## [1] TRUE
# Sort and identify key TFs
tf_summary <- motif_summary[order(motif_summary$motif_count, decreasing = TRUE), ]
top_tf_summary <- head(tf_summary, 121) # Adjust the number as required

# Mapping Entrez IDs to gene symbols
gene_symbols <- mapIds(org.Hs.eg.db, keys = rownames(top_tf_summary), column = "SYMBOL", keytype = "ENTREZID", multiVals = "first")
## 'select()' returned 1:1 mapping between keys and columns
# Replace rownames with gene symbols
rownames(top_tf_summary) <- gene_symbols

# Add reason ID as a column
top_tf_summary$motif_id <- rownames(top_tf_summary)

# Add to the table of TF names
motif1 <- merge(top_tf_summary, motif_info, by.x = "tf_name", by.y = "motif_id")

# Reorder columns
motif2 <- motif1[, c("motif_id", "tf_name.y", "motif_count")]
colnames(motif2) <- c("motif_id", "tf_name", "motif_count")

# Sort by frequency (motif_count) in descending order
motif2 <- motif2 %>% arrange(desc(motif_count))

print(motif2)
##   motif_id     tf_name motif_count
## 1  TNFAIP3    MAX::MYC         190
## 2      IL6        IRF2         148
## 3    DUSP4       FOXF2         144
## 4     OLR1 MZF1(var.2)         144
## 5     CD69       PPARG         131
## 6   CLEC4D       FOXD1         111

8. Comparison between peripheral blood samples from AS patients and control samples.

# Wald test to obtain contrast-specific results
dsd <- DESeq(dsa, test = "Wald", sfType = "poscount")
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 9 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
r <- results(dsd, contrast = c("Group", groups[2], groups[3]), alpha = 0.05, pAdjustMethod = "fdr")

groups <- levels(colData(dsd)$Group)

df <- as.data.frame(r)

# Filter only significant genes
sig_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) >= 1)

# volcano plot
old.pal <- palette(c("#00BFFF", "#FF3030")) # low-hi colors
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
  plot(log2FoldChange, -log10(padj), main=paste(groups[2], "vs", groups[3]),
       xlab="log2FC", ylab="-log10(Padj)", pch=20, cex=0.5)
  text(log2FoldChange, -log10(padj), labels=rownames(r), cex=0.6, pos=4)
})
with(subset(r, padj<0.05 & abs(log2FoldChange) >= 1),
     points(log2FoldChange, -log10(padj), pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1))
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20,col=1:2)

# Plot only significant genes
# MD PLOT
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
  plot(log10(baseMean), log2FoldChange,
       main=paste(groups[2], "vs", groups[3]),
       xlab="log10(mean of normalized counts)", ylab="log2FoldChange",
       pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1)
  text(log10(baseMean), log2FoldChange, labels=rownames(sig_genes), cex=0.6, pos=4)
})
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20, col=1:2)
abline(h=0)

palette(old.pal) # restore palette

# Add gene symbols to the points on the graph
# Install the packages if you do not already have them
library(ggplot2)
library(ggrepel)

plotVolcano <- function(res, title = "Volcano Plot") {
  res$group <- "NS"
  res$group[res$padj < 0.05 & res$log2FoldChange > 1] <- "Up"
  res$group[res$padj < 0.05 & res$log2FoldChange < -1] <- "Down"
  
  res$label <- ifelse(res$group != "NS", rownames(res), NA)
  
  ggplot(res, aes(x = log2FoldChange, y = -log10(padj), color = group)) +
    geom_point(alpha = 0.7, size = 2) +
    geom_hline(yintercept = -log10(0.05), linetype = "dashed") +
    geom_vline(xintercept = c(-1, 1), linetype = "dashed") +
    scale_color_manual(values = c("Up" = "firebrick", "Down" = "dodgerblue", "NS" = "grey80")) +
    ggrepel::geom_text_repel(aes(label = label), size = 3, max.overlaps = Inf) +
    theme_minimal() +
    labs(title = title, x = "log2 Fold Change", y = "-log10 adjusted p-value", color = "Regulation")
}

# Example of function usage
plotVolcano(r, paste(groups[2], "vs", groups[3]))
## Warning: Removed 62 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 409 rows containing missing values or values outside the scale range
## (`geom_text_repel()`).

# Genes upregulated
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange >= 1))

# Genes downregulated
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange <= -1))

# All DEGs with |log2FC| > 2
de_genes <- c(up_genes, down_genes)

expr_datasa <- as.data.frame(expr_data[rownames(expr_data) %in% de_genes, ])

# Convert expression data to long format for ggplot2
expr_datas <- as.data.frame(expr_datasa)
expr_datas$Gene <- rownames(expr_datas)
expr_datas <- pivot_longer(expr_datas, cols = -Gene, names_to = "Sample", values_to = "Expression")
expr_datas <- merge(expr_datas, pheno_data, by.x = "Sample", by.y = "geo_accession")

# Check column names and a sample of the data
expresse <- r[order(r$padj)[1:429], ]
expresse <- merge(as.data.frame(expresse), expr_datasa, by = 0, sort = F)


library(dplyr)
library(tibble)
library(clusterProfiler)
library(ggplot2)

r_df <- as.data.frame(r)

# Assuming that “r_df” is your data frame with the DESeq2 results

# This ensures that gene names are preserved.
r_df_com_genes <- r_df %>%
  rownames_to_column(var = "Gene") 

top30_fc <- r_df_com_genes %>%
  dplyr::filter(padj < 0.05 & abs(log2FoldChange) > 1) %>%
  dplyr::arrange(desc(abs(log2FoldChange))) %>%
  dplyr::slice(1:30) %>%
  dplyr::mutate(
    Regulation = case_when(
      log2FoldChange > 1 ~ "Upregulated",
      log2FoldChange < -1 ~ "Downregulated"
    )
  )

# Chart with positive and negative bars
ggplot(top30_fc, aes(x = reorder(Gene, log2FoldChange), y = log2FoldChange, fill = Regulation)) +
  geom_col() +
  coord_flip() + # Place the genes on the Y axis
  scale_fill_manual(values = c("Upregulated" = "steelblue", "Downregulated" = "tomato")) +
  scale_y_continuous(breaks = seq(-8, 4, by = 1)) + # Adjust the limits if necessary.
  theme_bw() +
  labs(
    title = "The most prominent DEGs between AS and Healthy (GSE117769)",
    x = "Gene",
    y = "log2 Fold Change",
    fill = "Regulation"
  ) + 
  theme(
    axis.text.y = element_text(color = "black", face = "bold", size = 9)
  )

# --- Selects the 20 MOST overexpressed genes ---
up_20genes <- expresse %>%
  filter(padj < 0.05 & log2FoldChange > 1) %>%
  arrange(desc(log2FoldChange)) %>% 
  head(20) %>%
  pull(Row.names)

# --- Filters expression data ---
expr_datas_filtrado_up <- expr_datas %>%
  filter(`characteristics_ch1.6` %in% c("phenotype: Ankylosing spondylitis", "phenotype: Healthy")) %>%
  filter(Gene %in% up_20genes)

# --- Calculates the average per gene and per group  ---
expr_datasa_up <- expr_datas_filtrado_up %>%
  group_by(Gene, `characteristics_ch1.6`) %>%
  summarise(
    mean_expression = mean(Expression, na.rm = TRUE),
    sd_expression = sd(Expression, na.rm = TRUE),
    .groups = 'drop'
  )

# --- Preparation for the chart ---
# Filter to show the average expression ONLY in the “non-lesion” group
dados_para_plotar_up <- expr_datasa_up %>%
  filter(characteristics_ch1.6 == "phenotype: Ankylosing spondylitis")

# --- Graph Generation ---
ggplot(dados_para_plotar_up, aes(x = mean_expression, y = reorder(Gene, mean_expression))) +
  geom_col(fill = "steelblue", color = "black", width = 0.7) +
  labs(
    title = "Average Expression of the Main Upregulated Genes in Ankylosing spondylitis", # Título mais claro
    subtitle = "For AS vs Healthy (GSE117769)",
    x = "Average Expression in the Group 'AS'", # Rótulo do eixo mais claro
    y = "Gene"
  ) +
  theme_minimal(base_size = 14) +
  theme(
    panel.grid.major.y = element_blank(),
    axis.text.y = element_text(size = 12)
  )

# --- Selects the 20 MOST under-expressed genes ---
down_20genes <- expresse %>%
  filter(padj < 0.05 & log2FoldChange < -1) %>%
  arrange(log2FoldChange) %>% # <-- Sort from most negative to least negative
  head(20) %>%
  pull(Row.names)

# --- Filters expression data for genes and groups of interest ---
expr_datas_filtrado_down <- expr_datas %>%
  filter(`characteristics_ch1.6` %in% c("phenotype: Ankylosing spondylitis", "phenotype: Healthy")) %>%
  filter(Gene %in% down_20genes)

# --- Calculates the average per gene and per group ---
expr_datasa_down <- expr_datas_filtrado_down %>%
  group_by(Gene, `characteristics_ch1.6`) %>%
  summarise(
    mean_expression = mean(Expression, na.rm = TRUE),
    .groups = 'drop'
  )

# --- Preparation for the chart ---
# Filter to show the average expression ONLY in the “lesion” group
dados_para_plotar <- expr_datasa_down %>%
  filter(characteristics_ch1.6 == "phenotype: Ankylosing spondylitis")

# --- Graph Generation ---
ggplot(dados_para_plotar, aes(x = mean_expression, y = reorder(Gene, -mean_expression))) +
  geom_col(fill = "red", color = "black", width = 0.7) +
  labs(
    title = "Average Expression of the Main Downregulated Genes in Ankylosing spondylitis", # Título mais claro
    subtitle = "For AS vs Healthy (GSE117769)",
    x = "Average Expression in the Group 'AS'", # Rótulo do eixo mais claro
    y = "Gene"
  ) +
  theme_minimal(base_size = 14) +
  theme(
    panel.grid.major.y = element_blank(),
    axis.text.y = element_text(size = 12)
  )

# --- The code to create 'count_array' ---
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange > 1))
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange < -1))
genes_interesse <- c(up_genes, down_genes)

expr_filtrado <- expr_datas %>%
  filter(`characteristics_ch1.6` %in% c("phenotype: Ankylosing spondylitis", "phenotype: Healthy")) %>%
  filter(Gene %in% genes_interesse)

matriz_contagem <- expr_filtrado %>%
  select(Gene, Sample, Expression) %>%
  pivot_wider(names_from = Sample, values_from = Expression, values_fill = 0) %>%
  column_to_rownames(var = "Gene")

# Filter your original “sample_info” object to keep only the samples that are in your final matrix
# This ensures that the annotation corresponds exactly to the heatmap data
sample_info_filtrado <- subset(sample_info, rownames(sample_info) %in% colnames(matriz_contagem))


# Select the 20 most highly expressed genes
media_dos_genes <- rowMeans(matriz_contagem)
media_ordenada <- sort(media_dos_genes, decreasing = TRUE)
top_20_genes_por_media <- names(head(media_ordenada, 20))
heatmapData_top20 <- as.matrix(matriz_contagem[top_20_genes_por_media, ])


# Create the annotation for the heatmap from the filtered and corrected information
annotation_data <- data.frame(
  Group = sample_info_filtrado$Group,
  row.names = rownames(sample_info_filtrado)
)

# Ensure that the order of the columns in the heatmap and annotation is the same
heatmapData_top20 <- heatmapData_top20[, rownames(annotation_data)]


# --- Heatmap generation with ComplexHeatmap ---

# Rescale data by row (Z-score)
mat_scaled <- t(scale(t(heatmapData_top20)))

# Create the column annotation
ha_col <- HeatmapAnnotation(
  Group = annotation_data$Group,
  col = list(Group = c("AS" = "#1f77b4", "Healthy" = "yellow"))
)

# Define the colour palette
cores <- colorRamp2(c(-2, 0, 2), rev(RColorBrewer::brewer.pal(3, "RdBu")))

# Generate the heatmap
Heatmap(
  mat_scaled,
  name = "Z-score",
  top_annotation = ha_col,
  col = cores,
  
  # Divide the columns into groups for clearer viewing
  column_split = annotation_data$Group,
  
  cluster_rows = TRUE,
  cluster_columns = TRUE, # Cluster within each divided group
  
  show_column_names = FALSE,
  show_row_names = TRUE,
  column_title = "Heatmap of the most highly expressed DEGs (AS vs. Healthy GSE117769)",
  heatmap_legend_param = list(title = "Z-score")
)

# Filter differentially expressed genes
de_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) > 1)

#Create a data frame from de_genes
de_genes <- data.frame(de_genes)

# Suppose your dataframe is called df and you want to select columns ‘column1’, “column2” and ‘column3’
de_genes <- de_genes %>% select(log2FoldChange, padj)

# Assuming that rownames(df) are gene symbols
gene_symbols <- rownames(de_genes)

# Convert gene symbols to Entrez IDs
gene_entrez_ids <- bitr(gene_symbols, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)
## 'select()' returned 1:1 mapping between keys and columns
# First, convert the rownames from df into a column
de_genes$Symbol <- rownames(de_genes)

# Performs the join between the original table and the converted IDs
de_genes <- merge(de_genes, gene_entrez_ids, by.x = "Symbol", by.y = "SYMBOL", all.x = TRUE)

# Ensure unique symbols
de_genes <- de_genes[!duplicated(de_genes$ENTREZID), ]

# Alternative Workflow with STRINGdb Integration in R
# Initialise the STRINGdb object for a specific organism
string_db <- STRINGdb$new(version = "12", species = 9606, score_threshold = 400, input_directory = "")

options(timeout = 600)  # increases to 10 minutes

# Gene mapping using STRINGdb
mapped_genes <- string_db$map(de_genes, "Symbol", removeUnmappedRows = TRUE)

# Recover interactions for mapped genes
interactions <- string_db$get_interactions(mapped_genes$STRING_id)

# Visualise the network using igraph or other visualisation tools
library(igraph)
g <- graph_from_data_frame(interactions, directed=FALSE)
plot(g)

# Detect clusters (e.g. Louvain)
clusters <- cluster_louvain(g)

# Plot with colours by cluster
plot(g, vertex.color=clusters$membership)

# Perform GO enrichment analysis
# Biological Process
enrich_result <- enrichGO(gene = mapped_genes$Symbol,
                          OrgDb = org.Hs.eg.db,
                          keyType = "SYMBOL",
                          ont = "BP", # Biological Ontology. It can be ‘BP’, “MF”, or ‘CC’.
                          pAdjustMethod = "BH",
                          pvalueCutoff = 0.05,
                          qvalueCutoff = 0.2)

barplot(enrich_result, showCategory = 10, title= "GO Enrichment Analysis")
## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?

# Network graph of enriched terms
cnetplot(enrich_result, showCategory = 10)

# Heatmap
heatplot(enrich_result, showCategory = 10)

# Perform KEGG enrichment analysis
ekegg <- enrichKEGG(gene = mapped_genes$ENTREZID, organism = "hsa", pAdjustMethod = "BH", qvalueCutoff = 0.05)

# Generate GO/STRING style bubble chart
if (is.null(ekegg) || nrow(as.data.frame(ekegg)) == 0) {
  print("No significantly enriched KEGG pathways were found with the criteria provided.")
} else {
  plot_data_kegg <- as.data.frame(ekegg) %>%
    arrange(p.adjust) %>% # Sort by p.adjust (FDR)
    head(15) # Selects the 15 most significant pathways to plot

  # Creates a numerical position for the terms on the Y-axis, to control the order and lines
  plot_data_kegg$y_pos <- rev(seq_along(plot_data_kegg$Description)) # reverse to the most significant at the top
  
  # Starting to build the graph with ggplot2
  ggplot(plot_data_kegg, aes(x = Count, y = y_pos)) +
    # Adds the connection lines (wires) from the Y-axis to the bubble
    geom_segment(aes(x = 0, xend = Count, y = y_pos, yend = y_pos),
                 color = "gray80", linewidth = 0.6) + # Softer colour for the lines
    # Add the bubbles
    geom_point(aes(size = Count, color = p.adjust), alpha = 0.9) +
    # Colour scale configuration for FDR (p.adjust)
    scale_color_gradientn(
      colors = c("darkblue", "steelblue", "lightblue", "lightgreen", "yellow", "orange", "darkred"),
      name = "FDR",
      trans = "log10", # Use logarithmic scale for FDR
      breaks = scales::trans_breaks("log10", function(x) 10^x), # Breaks in scientific notation captions
      labels = scales::trans_format("log10", scales::math_format(10^.x)), # Scientific notation format
      limits = c(min(plot_data_kegg$p.adjust), max(plot_data_kegg$p.adjust)) # Sets limits for data
    ) +
    # Size scale configuration for Gene Counting
    scale_size_area(
      max_size = 18, # Maximum bubble size
      name = "Gene count", # Caption title size
      breaks = unique(round(quantile(plot_data_kegg$Count, probs = c(0.25, 0.5, 0.75, 1.0)))), # Suggests reasonable breaks
      labels = unique(round(quantile(plot_data_kegg$Count, probs = c(0.25, 0.5, 0.75, 1.0))))
    ) +
    # Maps the Y-axis labels back to the KEGG pathway descriptions
    scale_y_continuous(
      breaks = plot_data_kegg$y_pos,
      labels = plot_data_kegg$Description
    ) +
    # Labels and Chart Title
    labs(
      title = "KEGG Pathway Enrichment Analysis",
      x = "Gene count", # X-axis is now Gene Count
      y = "KEGG Pathway" # Y-axis is the name of the pathway
    ) +
    # Chart Theme and Style
    theme_minimal() +
    theme(
      axis.text.y = element_text(size = 12, face = "bold"), # KEGG terms in bold and larger font
      axis.title = element_text(size = 14, face = "bold"), # Axis titles
      plot.title = element_text(size = 16, face = "bold", hjust = 0.5), # Centred title
      legend.position = "right", # Position of subtitles
      legend.title = element_text(size = 12, face = "bold"),
      legend.text = element_text(size = 10),
      panel.grid.major.y = element_blank(), # Remove standard horizontal grid lines
      panel.grid.minor = element_blank(), # Remove smaller grid lines
      panel.border = element_rect(colour = "black", fill=NA, linewidth=1.2) # Black border around the plot
    )
} 

barplot(ekegg, showCategory = 10, title = "KEGG Enrichment Analysis")
## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?

# Network graph of enriched terms
cnetplot(ekegg, showCategory = 10)

# Heatmap
heatplot(ekegg, showCategory = 10)

9. Transcription factors between the analysis of AS vs Healthy

# Load the TxDb database
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene

# Extraction of exons by gene
exons_by_gene <- exonsBy(txdb, by = "gene")

# Obtain the coordinates of the genes (taking the first and last positions of the exons)
genes_info <- range(exons_by_gene)

# Obtain transcription information
transcripts_info <- transcripts(txdb)

# Map genes of interest to Entrez IDs (replace “de_genes” with the actual list of genes)
gene_entrez <- mapIds(org.Hs.eg.db, keys = mapped_genes$Symbol, column = "ENTREZID", keytype = "SYMBOL", multiVals = "first")
## 'select()' returned 1:1 mapping between keys and columns
# Filter the genes of interest
promoters_info <- subset(genes_info, names(genes_info) %in% gene_entrez)

# Define promoter regions (2 kb upstream of TSS)
promoters <- promoters(promoters_info, upstream = 2000, downstream = 0)

# Filter the main chromosomes
promoters <- keepStandardChromosomes(promoters, pruning.mode = "coarse")

# Remove any regions that exceed the limits of the chromosomes.
promoters <- trim(promoters)

# Convert CompressedGRangesList promoters to GRanges
promoters_gr <- unlist(promoters)

# Load the JASPAR grounds database
motifs <- getMatrixSet(JASPAR2020, opts = list(species = "Homo sapiens"))

# Create a data frame with the IDs of the reasons and their names (TFs)
motif_info <- data.frame(
  motif_id = names(motifs),
  tf_name = sapply(motifs, function(x) x@name),
  stringsAsFactors = FALSE
)

# Enriching motifs in promoting regions
motifHits <- matchMotifs(motifs, promoters_gr, genome = BSgenome.Hsapiens.UCSC.hg38)

# Count the number of occurrences of the reasons in each promoting region
motif_counts <- countOverlaps(promoters_gr, motifHits)

# Add counts to GRanges with promoting regions
promoters_gr$motif_counts <- motif_counts

# Summary of motif counts
summary(promoters_gr$motif_counts)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.0000  0.0000  0.0000  0.4737  1.0000  1.0000
# Obtain the names of the motifs and TFs
motif_names <- names(motifHits)

# Extract the reason table from the RangedSummarizedExperiment object
motif_data <- assays(motifHits)[[1]] # Assuming that the table of reasons is in the first list of assays

# Obtain information about TFs
# The names of the TFs can be in the colnames or in associated metadata
tf_names <- colnames(motif_data)  

# Add the reason count if available
motif_counts <- rowSums(motif_data) # Count the occurrence of motifs (adjust as necessary)

# Check the dimensions of the motif_data object
dim(motif_data) # Number of rows and columns
## [1]  19 633
# Check the length of tf_names and motif_counts
tf_names_length <- length(tf_names)
motif_counts_length <- length(motif_counts)

# Print the lengths for diagnosis
cat("Length of tf_names:", tf_names_length, "\n")
## Length of tf_names: 633
cat("Length of motif_counts:", motif_counts_length, "\n")
## Length of motif_counts: 19
# Verify that the dimensions of motif_data correspond to the number of TFs and motifs
motif_data_dims <- dim(motif_data)
cat("Dimensions of motif_data (rows, columns):", motif_data_dims, "\n")
## Dimensions of motif_data (rows, columns): 19 633
# Check whether the number of reasons is greater or lesser
if (tf_names_length > motif_counts_length) {
  # Check additional columns
  tf_names <- tf_names[1:motif_counts_length] # Adjust to the length of motif_counts
} else {
  # Adjust motif_counts to match tf_names
  motif_counts <- motif_counts[1:tf_names_length]
}

# Now, I have created the data frame with adjusted lengths
motif_summary <- data.frame(
  tf_name = tf_names,
  motif_count = motif_counts
)

# Check the correspondence between TF names and the columns in motif_data
all(tf_names %in% colnames(motif_data)) # Should return TRUE if all TF names are present
## [1] TRUE
# Sort and identify key TFs
tf_summary <- motif_summary[order(motif_summary$motif_count, decreasing = TRUE), ]
top_tf_summary <- head(tf_summary, 130) # Adjust the number as required.

# Mapping Entrez IDs to gene symbols
gene_symbols <- mapIds(org.Hs.eg.db, keys = rownames(top_tf_summary), column = "SYMBOL", keytype = "ENTREZID", multiVals = "first")
## 'select()' returned 1:1 mapping between keys and columns
# Replace rownames with gene symbols
rownames(top_tf_summary) <- gene_symbols

top_tf_summary$motif_id <- rownames(top_tf_summary)

# Combine with the table of TF names
motif1 <- merge(top_tf_summary, motif_info, by.x = "tf_name", by.y = "motif_id")

# Reorganise columns for better viewing
motif2<- motif1[, c("motif_id", "tf_name.y", "motif_count")]
colnames(motif2) <- c("motif_id", "tf_name.y", "motif_count")

# View
print(motif2)
##    motif_id   tf_name.y motif_count
## 1      GJB6       FOXF2         173
## 2      CCR6       FOXD1         103
## 3      CCR7        IRF2         206
## 4     DDIT3 MZF1(var.2)         139
## 5       FOS    MAX::MYC         152
## 6     CXCL2       PPARG         182
## 7      IFNG        PAX6         128
## 8     CXCL8        PBX1         218
## 9       JUN        RORA         142
## 10     JUNB RORA(var.2)         118
## 11     AREG       RREB1         182
## 12      MYC   RXRA::VDR         153
## 13     PER1        SOX9         144
## 14     RORC         SRY         170
## 15     CCL2  TAL1::TCF3         102
## 16  TNFAIP3         REL         198
## 17    ZFP36        RELA         126
## 18    FOSL1 NR1H2::RXRA         117
## 19     CD69  NFIC::TLX1         137

10. Comparison between peripheral blood samples from AS patients and PsA patients.

# Wald test to obtain contrast-specific results
dsd <- DESeq(dsa, test = "Wald", sfType = "poscount")
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 9 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
r <- results(dsd, contrast = c("Group", groups[2], groups[1]), alpha = 0.05, pAdjustMethod = "fdr")

groups <- levels(colData(dsd)$Group)

df <- as.data.frame(r)

# Filter only significant genes
sig_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) >= 1)

# volcano plot
old.pal <- palette(c("#00BFFF", "#FF3030")) # low-hi colors
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
  plot(log2FoldChange, -log10(padj), main=paste(groups[2], "vs", groups[1]),
       xlab="log2FC", ylab="-log10(Padj)", pch=20, cex=0.5)
  text(log2FoldChange, -log10(padj), labels=rownames(r), cex=0.6, pos=4)
})
with(subset(r, padj<0.05 & abs(log2FoldChange) >= 1),
     points(log2FoldChange, -log10(padj), pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1))
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20,col=1:2)

# Plot only significant genes
# MD PLOT
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
  plot(log10(baseMean), log2FoldChange,
       main=paste(groups[2], "vs", groups[1]),
       xlab="log10(mean of normalized counts)", ylab="log2FoldChange",
       pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1)
  text(log10(baseMean), log2FoldChange, labels=rownames(sig_genes), cex=0.6, pos=4)
})
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20, col=1:2)
abline(h=0)

palette(old.pal) # restore palette

# Add gene symbols to the points on the graph
# Install the packages if you do not already have them
library(ggplot2)
library(ggrepel)

plotVolcano <- function(res, title = "Volcano Plot") {
  res$group <- "NS"
  res$group[res$padj < 0.05 & res$log2FoldChange > 1] <- "Up"
  res$group[res$padj < 0.05 & res$log2FoldChange < -1] <- "Down"
  
  res$label <- ifelse(res$group != "NS", rownames(res), NA)
  
  ggplot(res, aes(x = log2FoldChange, y = -log10(padj), color = group)) +
    geom_point(alpha = 0.7, size = 2) +
    geom_hline(yintercept = -log10(0.05), linetype = "dashed") +
    geom_vline(xintercept = c(-1, 1), linetype = "dashed") +
    scale_color_manual(values = c("Up" = "firebrick", "Down" = "dodgerblue", "NS" = "grey80")) +
    ggrepel::geom_text_repel(aes(label = label), size = 3, max.overlaps = Inf) +
    theme_minimal() +
    labs(title = title, x = "log2 Fold Change", y = "-log10 adjusted p-value", color = "Regulation")
}

# Example of function usage
plotVolcano(r, paste(groups[2], "vs", groups[1]))
## Warning: Removed 78 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 424 rows containing missing values or values outside the scale range
## (`geom_text_repel()`).

# Genes upregulated
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange >= 1))

# Genes downregulated
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange <= -1))

# All DEGs with |log2FC| > 2
de_genes <- c(up_genes, down_genes)

expr_datasa <- as.data.frame(expr_data[rownames(expr_data) %in% de_genes, ])

# Convert expression data to long format for ggplot2
expr_datas <- as.data.frame(expr_datasa)
expr_datas$Gene <- rownames(expr_datas)
expr_datas <- pivot_longer(expr_datas, cols = -Gene, names_to = "Sample", values_to = "Expression")
expr_datas <- merge(expr_datas, pheno_data, by.x = "Sample", by.y = "geo_accession")

# Check column names and a sample of the data
expresse <- r[order(r$padj)[1:429], ]
expresse <- merge(as.data.frame(expresse), expr_datasa, by = 0, sort = F)


library(dplyr)
library(tibble)
library(clusterProfiler)
library(ggplot2)

r_df <- as.data.frame(r)

# Assuming that “r_df” is your data frame with the DESeq2 results

# This ensures that gene names are preserved.
r_df_com_genes <- r_df %>%
  rownames_to_column(var = "Gene") 

top30_fc <- r_df_com_genes %>%
  dplyr::filter(padj < 0.05 & abs(log2FoldChange) > 1) %>%
  dplyr::arrange(desc(abs(log2FoldChange))) %>%
  dplyr::slice(1:30) %>%
  dplyr::mutate(
    Regulation = case_when(
      log2FoldChange > 1 ~ "Upregulated",
      log2FoldChange < -1 ~ "Downregulated"
    )
  )

# Chart with positive and negative bars
ggplot(top30_fc, aes(x = reorder(Gene, log2FoldChange), y = log2FoldChange, fill = Regulation)) +
  geom_col() +
  coord_flip() + # Place the genes on the Y axis
  scale_fill_manual(values = c("Upregulated" = "steelblue", "Downregulated" = "tomato")) +
  scale_y_continuous(breaks = seq(-8, 4, by = 1)) + # Adjust the limits if necessary.
  theme_bw() +
  labs(
    title = "The most prominent DEGs between AS and PsA (GSE117769)",
    x = "Gene",
    y = "log2 Fold Change",
    fill = "Regulation"
  ) + 
  theme(
    axis.text.y = element_text(color = "black", face = "bold", size = 9)
  )

# --- Selects the 20 MOST overexpressed genes ---
up_20genes <- expresse %>%
  filter(padj < 0.05 & log2FoldChange > 1) %>%
  arrange(desc(log2FoldChange)) %>% 
  head(20) %>%
  pull(Row.names)

# --- Filters expression data ---
expr_datas_filtrado_up <- expr_datas %>%
  filter(`characteristics_ch1.6` %in% c("phenotype: Ankylosing spondylitis", "phenotype: Psoriatic arthritis")) %>%
  filter(Gene %in% up_20genes)

# --- Calculates the average per gene and per group  ---
expr_datasa_up <- expr_datas_filtrado_up %>%
  group_by(Gene, `characteristics_ch1.6`) %>%
  summarise(
    mean_expression = mean(Expression, na.rm = TRUE),
    sd_expression = sd(Expression, na.rm = TRUE),
    .groups = 'drop'
  )

# --- Preparation for the chart ---
# Filter to show the average expression ONLY in the “non-lesion” group
dados_para_plotar_up <- expr_datasa_up %>%
  filter(characteristics_ch1.6 == "phenotype: Ankylosing spondylitis")

# --- Graph Generation ---
ggplot(dados_para_plotar_up, aes(x = mean_expression, y = reorder(Gene, mean_expression))) +
  geom_col(fill = "steelblue", color = "black", width = 0.7) +
  labs(
    title = "Average Expression of the Main Upregulated Genes in Ankylosing spondylitis", # Título mais claro
    subtitle = "For AS vs PsA (GSE117769)",
    x = "Average Expression in the Group 'AS'", # Rótulo do eixo mais claro
    y = "Gene"
  ) +
  theme_minimal(base_size = 14) +
  theme(
    panel.grid.major.y = element_blank(),
    axis.text.y = element_text(size = 12)
  )

# --- Selects the 20 MOST under-expressed genes ---
down_20genes <- expresse %>%
  filter(padj < 0.05 & log2FoldChange < -1) %>%
  arrange(log2FoldChange) %>% # <-- Sort from most negative to least negative
  head(20) %>%
  pull(Row.names)

# --- Filters expression data for genes and groups of interest ---
expr_datas_filtrado_down <- expr_datas %>%
  filter(`characteristics_ch1.6` %in% c("phenotype: Ankylosing spondylitis", "phenotype: Psoriatic arthritis")) %>%
  filter(Gene %in% down_20genes)

# --- Calculates the average per gene and per group ---
expr_datasa_down <- expr_datas_filtrado_down %>%
  group_by(Gene, `characteristics_ch1.6`) %>%
  summarise(
    mean_expression = mean(Expression, na.rm = TRUE),
    .groups = 'drop'
  )

# --- Preparation for the chart ---
# Filter to show the average expression ONLY in the “lesion” group
dados_para_plotar <- expr_datasa_down %>%
  filter(characteristics_ch1.6 == "phenotype: Ankylosing spondylitis")

# --- Graph Generation ---
ggplot(dados_para_plotar, aes(x = mean_expression, y = reorder(Gene, -mean_expression))) +
  geom_col(fill = "red", color = "black", width = 0.7) +
  labs(
    title = "Average Expression of the Main Downregulated Genes in Ankylosing spondylitis", # Título mais claro
    subtitle = "For AS vs PsA (GSE117769)",
    x = "Average Expression in the Group 'AS'", # Rótulo do eixo mais claro
    y = "Gene"
  ) +
  theme_minimal(base_size = 14) +
  theme(
    panel.grid.major.y = element_blank(),
    axis.text.y = element_text(size = 12)
  )

# --- The code to create 'count_array' ---
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange > 1))
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange < -1))
genes_interesse <- c(up_genes, down_genes)

expr_filtrado <- expr_datas %>%
  filter(`characteristics_ch1.6` %in% c("phenotype: Ankylosing spondylitis", "phenotype: Psoriatic arthritis")) %>%
  filter(Gene %in% genes_interesse)

matriz_contagem <- expr_filtrado %>%
  select(Gene, Sample, Expression) %>%
  pivot_wider(names_from = Sample, values_from = Expression, values_fill = 0) %>%
  column_to_rownames(var = "Gene")

# Filter your original “sample_info” object to keep only the samples that are in your final matrix
# This ensures that the annotation corresponds exactly to the heatmap data
sample_info_filtrado <- subset(sample_info, rownames(sample_info) %in% colnames(matriz_contagem))


# Select the 20 most highly expressed genes
media_dos_genes <- rowMeans(matriz_contagem)
media_ordenada <- sort(media_dos_genes, decreasing = TRUE)
top_20_genes_por_media <- names(head(media_ordenada, 20))
heatmapData_top20 <- as.matrix(matriz_contagem[top_20_genes_por_media, ])


# Create the annotation for the heatmap from the filtered and corrected information
annotation_data <- data.frame(
  Group = sample_info_filtrado$Group,
  row.names = rownames(sample_info_filtrado)
)

# Ensure that the order of the columns in the heatmap and annotation is the same
heatmapData_top20 <- heatmapData_top20[, rownames(annotation_data)]


# --- Heatmap generation with ComplexHeatmap ---

# Rescale data by row (Z-score)
mat_scaled <- t(scale(t(heatmapData_top20)))

# Create the column annotation
ha_col <- HeatmapAnnotation(
  Group = annotation_data$Group,
  col = list(Group = c("AS" = "#1f77b4", "PsA" = "yellow"))
)

# Define the colour palette
cores <- colorRamp2(c(-2, 0, 2), rev(RColorBrewer::brewer.pal(3, "RdBu")))

# Generate the heatmap
Heatmap(
  mat_scaled,
  name = "Z-score",
  top_annotation = ha_col,
  col = cores,
  
  # Divide the columns into groups for clearer viewing
  column_split = annotation_data$Group,
  
  cluster_rows = TRUE,
  cluster_columns = TRUE, # Cluster within each divided group
  
  show_column_names = FALSE,
  show_row_names = TRUE,
  column_title = "Heatmap of the most highly expressed DEGs (AS vs. PsA GSE117769)",
  heatmap_legend_param = list(title = "Z-score")
)

# Filter differentially expressed genes
de_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) > 1)

#Create a data frame from de_genes
de_genes <- data.frame(de_genes)

# Suppose your dataframe is called df and you want to select columns ‘column1’, “column2” and ‘column3’
de_genes <- de_genes %>% select(log2FoldChange, padj)

# Assuming that rownames(df) are gene symbols
gene_symbols <- rownames(de_genes)

# Convert gene symbols to Entrez IDs
gene_entrez_ids <- bitr(gene_symbols, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)
## 'select()' returned 1:1 mapping between keys and columns
# First, convert the rownames from df into a column
de_genes$Symbol <- rownames(de_genes)

# Performs the join between the original table and the converted IDs
de_genes <- merge(de_genes, gene_entrez_ids, by.x = "Symbol", by.y = "SYMBOL", all.x = TRUE)

# Ensure unique symbols
de_genes <- de_genes[!duplicated(de_genes$ENTREZID), ]

# Alternative Workflow with STRINGdb Integration in R
# Initialise the STRINGdb object for a specific organism
string_db <- STRINGdb$new(version = "12", species = 9606, score_threshold = 400, input_directory = "")

options(timeout = 600)  # increases to 10 minutes

# Gene mapping using STRINGdb
mapped_genes <- string_db$map(de_genes, "Symbol", removeUnmappedRows = TRUE)

# Recover interactions for mapped genes
interactions <- string_db$get_interactions(mapped_genes$STRING_id)

# Visualise the network using igraph or other visualisation tools
library(igraph)
g <- graph_from_data_frame(interactions, directed=FALSE)
plot(g)

# Detect clusters (e.g. Louvain)
clusters <- cluster_louvain(g)

# Plot with colours by cluster
plot(g, vertex.color=clusters$membership)

# Perform GO enrichment analysis
# Biological Process
enrich_result <- enrichGO(gene = mapped_genes$Symbol,
                          OrgDb = org.Hs.eg.db,
                          keyType = "SYMBOL",
                          ont = "BP", # Biological Ontology. It can be ‘BP’, “MF”, or ‘CC’.
                          pAdjustMethod = "BH",
                          pvalueCutoff = 0.05,
                          qvalueCutoff = 0.2)

barplot(enrich_result, showCategory = 10, title= "GO Enrichment Analysis")
## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?

# Network graph of enriched terms
cnetplot(enrich_result, showCategory = 10)

# Heatmap
heatplot(enrich_result, showCategory = 10)

11. Transcription factors between the analysis of AS vs PsA.

# Load the TxDb database
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene

# Extraction of exons by gene
exons_by_gene <- exonsBy(txdb, by = "gene")

# Obtain the coordinates of the genes (taking the first and last positions of the exons)
genes_info <- range(exons_by_gene)

# Obtain transcription information
transcripts_info <- transcripts(txdb)

# Map genes of interest to Entrez IDs (replace “de_genes” with the actual list of genes)
gene_entrez <- mapIds(org.Hs.eg.db, keys = mapped_genes$Symbol, column = "ENTREZID", keytype = "SYMBOL", multiVals = "first")
## 'select()' returned 1:1 mapping between keys and columns
# Filter the genes of interest
promoters_info <- subset(genes_info, names(genes_info) %in% gene_entrez)

# Define promoter regions (2 kb upstream of TSS)
promoters <- promoters(promoters_info, upstream = 2000, downstream = 0)

# Filter the main chromosomes
promoters <- keepStandardChromosomes(promoters, pruning.mode = "coarse")

# Remove any regions that exceed the limits of the chromosomes.
promoters <- trim(promoters)

# Convert CompressedGRangesList promoters to GRanges
promoters_gr <- unlist(promoters)

# Load the JASPAR grounds database
motifs <- getMatrixSet(JASPAR2020, opts = list(species = "Homo sapiens"))

# Create a data frame with the IDs of the reasons and their names (TFs)
motif_info <- data.frame(
  motif_id = names(motifs),
  tf_name = sapply(motifs, function(x) x@name),
  stringsAsFactors = FALSE
)

# Enriching motifs in promoting regions
motifHits <- matchMotifs(motifs, promoters_gr, genome = BSgenome.Hsapiens.UCSC.hg38)

# Count the number of occurrences of the reasons in each promoting region
motif_counts <- countOverlaps(promoters_gr, motifHits)

# Add counts to GRanges with promoting regions
promoters_gr$motif_counts <- motif_counts

# Summary of motif counts
summary(promoters_gr$motif_counts)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##       1       1       1       1       1       1
# Obtain the names of the motifs and TFs
motif_names <- names(motifHits)

# Extract the reason table from the RangedSummarizedExperiment object
motif_data <- assays(motifHits)[[1]] # Assuming that the table of reasons is in the first list of assays

# Obtain information about TFs
# The names of the TFs can be in the colnames or in associated metadata
tf_names <- colnames(motif_data)  

# Add the reason count if available
motif_counts <- rowSums(motif_data) # Count the occurrence of motifs (adjust as necessary)

# Check the dimensions of the motif_data object
dim(motif_data) # Number of rows and columns
## [1]   4 633
# Check the length of tf_names and motif_counts
tf_names_length <- length(tf_names)
motif_counts_length <- length(motif_counts)

# Print the lengths for diagnosis
cat("Length of tf_names:", tf_names_length, "\n")
## Length of tf_names: 633
cat("Length of motif_counts:", motif_counts_length, "\n")
## Length of motif_counts: 4
# Verify that the dimensions of motif_data correspond to the number of TFs and motifs
motif_data_dims <- dim(motif_data)
cat("Dimensions of motif_data (rows, columns):", motif_data_dims, "\n")
## Dimensions of motif_data (rows, columns): 4 633
# Check whether the number of reasons is greater or lesser
if (tf_names_length > motif_counts_length) {
  # Check additional columns
  tf_names <- tf_names[1:motif_counts_length] # Adjust to the length of motif_counts
} else {
  # Adjust motif_counts to match tf_names
  motif_counts <- motif_counts[1:tf_names_length]
}

# Now, I have created the data frame with adjusted lengths
motif_summary <- data.frame(
  tf_name = tf_names,
  motif_count = motif_counts
)

# Check the correspondence between TF names and the columns in motif_data
all(tf_names %in% colnames(motif_data)) # Should return TRUE if all TF names are present
## [1] TRUE
# Sort and identify key TFs
tf_summary <- motif_summary[order(motif_summary$motif_count, decreasing = TRUE), ]
top_tf_summary <- head(tf_summary, 130) # Adjust the number as required.

# Mapping Entrez IDs to gene symbols
gene_symbols <- mapIds(org.Hs.eg.db, keys = rownames(top_tf_summary), column = "SYMBOL", keytype = "ENTREZID", multiVals = "first")
## 'select()' returned 1:1 mapping between keys and columns
# Replace rownames with gene symbols
rownames(top_tf_summary) <- gene_symbols

top_tf_summary$motif_id <- rownames(top_tf_summary)

# Combine with the table of TF names
motif1 <- merge(top_tf_summary, motif_info, by.x = "tf_name", by.y = "motif_id")

# Reorganise columns for better viewing
motif2<- motif1[, c("motif_id", "tf_name.y", "motif_count")]
colnames(motif2) <- c("motif_id", "tf_name.y", "motif_count")

# View
print(motif2)
##   motif_id   tf_name.y motif_count
## 1     CCR6       FOXF2         100
## 2   CLEC4D       FOXD1         107
## 3     MMP9        IRF2         180
## 4     RETN MZF1(var.2)         111